The fork head domain is a conserved DNA-binding domain (also known as a "winged helix") of about 100 amino-acid residues.Drosophila melanogaster fork head protein is a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors [
]. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [
,
,
].The fork head domain binds B-DNA as a monomer [
], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].
Glutamyl-tRNA(Gln) amidotransferase (Gat;
) provides a means of producing correctly charged Gln-tRNA(Gln) through the transamidation of mis-acylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase [
,
]. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The enzyme is composed of three subunits: A (an amidase), B and C. It also exists in eukaryotes as a protein targeted to the mitochondria.The heterotrimer GatABC is involved in converting Glu to Gln and/or Asp to Asn, when the amino acid is attached to the appropriate tRNA. In Lactobacillus, GatABC is responsible for producing tRNA(Gln). In Archaea, GatABC is responsible for producing tRNA(Asn), while GatDE is responsible for producing tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyses both tRNA(Gln) and tRNA(Asn).This entry represents the extreme C-terminal structural domain of GatB and GatE subunits. It forms a predominantly α-helical structure.
NADH:ubiquinone oxidoreductase (complex I) (
) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) [
]. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondria, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins [].This entry represents subunit 15 of NADH-quinone oxidoreductase, also known as Complex I. The nqo15 subunit has probably a role in complex stabilisation, and may be also involved in the storage of iron for iron-sulphur cluster regeneration in the complex [
].
Bacterial light-harvesting complexes are also known as the antenna complexes. This entry represents the membrane all-alpha fold found in the alpha- and beta-chains of the antenna complexes.The antenna complexes of photosynthetic bacteria function as light-harvesting systems that absorb light and transfer the excitation energy to the reaction centres. The antenna complexes usually comprise 2 polypeptides (alpha- and beta-chains), 2-3 bacteriochlorophyll molecules and some carotenoids [
,
].The alpha- and beta-chains are small proteins of 40-70 residues. Each has an N-terminal hydrophilic cytoplasmic domain, a single transmembrane (TM) region, and a small C-terminal hydrophilic periplasmic domain. In both chains, the TM domain houses a conserved His residue, presumed to be involved in binding the magnesium atom of a bacteriochlorophyll group. The beta-chains are characterised by a further histidine at the C-terminal extremity of the cytoplasmic domain, which is also thought to be involved in bacteriochlorophyll binding.
This domain is found in several bacterial cytotoxic necrotizing factor proteins as well as related dermonecrotic toxin (DNT) from Bordetella species [
].Cytotoxic necrotizing factor 1 (CNF1) is a toxin whose structure from Escherichia coli revealed a 4-layer alpha/beta/beta/alpha structure containing mixed β-sheets [
]. CNF1 is expressed in strains of E. coli causing uropathogenic and neonatal meningitis. CNF1 alters host cell actin cytoskeleton and promotes bacterial invasion of the blood-brain barrier endothelial cells []. CNF1 belongs to a unique group of large cytotoxins that cause constitutive activation of Rho guanosine triphosphatases (GTPases), which are key regulators of the actin cytoskeleton [].Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain [
].
EspG and VirA are delivered into infected host epithelial cells by a type III secretory system [
,
]. These proteins function through the disruption of the host cell microtubule network []. VirA acts as a cysteine protease () on alpha-tubulin, a major component of microtubules, in order to destabilise surrounding microtubules and invade the cytoplasm of their target host cells [
]. VirA also promotes the formation of membrane ruffles through the activation of host rac1, which is associated with the destruction of microtubule networks []. In this way, VirA creates a tunnel inside the host cell cytoplasm by breaking down the microtubule infrastructure, which facilitates the bacterium's movement through the cytoplasm and also helps other bacteria move faster during the invasion of the eukaryotic cell.This superfamily family represents the N-terminal domain of VirA/EspG. Structurally, this domain consists of 4 beta strands and 2 alpha helices.
This entry represents the BT domain from plant Methylcrotonoyl-CoA carboxylase subunit alpha (MCCA), located between the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains. This domain mediates crucial interactions between the BC domain in the the alpha subunit and the carboxyltransferase (CT) domain in the beta subunit of this enzyme which are based on ion-pair, hydrogen-bonding and hydrophobic interactions. This domain has a backbone fold with a long helix surrounded by an eight-stranded anti-parallel beta barrel. There is a hook comprising the C-terminal part of the helix and the loop connecting it to the first strand of the beta barrel, which appears to have a central role in alpha and beta subunits interactions [
,
,
].In Arabidopsis, methylcrotonoyl-CoA carboxylase is involved in the catabolism of leucine, associated with reproductive growth. It may also participate in the catabolism of isoprenoids [
].
Methylglyoxal synthase (MGS) catalyses the conversion of dihydroxyacetone phosphate (DHAP) to methylglyoxal and phosphate:Glycerone phosphate = methylglyoxal + phosphate
The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilise DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterised by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria [
]. MGS is a small protein of about 13 to 17kDa. An aspartate residue is involved in the catalytic mechanism [].This entry represents a short conserved region that contains an aspartate residue involved in catalytic activty.
Prp8 is the largest and most highly conserved spliceosomal protein and is considered a master regulator of the spliceosome. It forms a salt-stable complex with the Brr2 helicase that is required for spliceosome catalytic activation and disassembly, and with the Snu114 GTPase that regulates Brr2 activity. Prp8 consists of a phylogenetically conserved Rnase H fold along with Prp8-specific elements. The function of this domain is to help assemble and stabilise the spliceosomal catalytic core and coordinate the activities of other splicing factors [
]. The overall structure of Rnase H is reminiscent of a left-hand mitten, in which a central six-stranded mixed β-sheet and the surrounding α-helices of the N-terminal domain correspond to the palm, an extended β-hairpin of the N-terminal domain comprises the thumb and the α-helical C-terminal domain represents the fingers []. This entry represents the all-helical fingers region of the Rnase H domain.
Prp8 is the largest and most highly conserved spliceosomal protein and is considered a master regulator of the spliceosome. It forms a salt-stable complex with the Brr2 helicase that is required for spliceosome catalytic activation and disassembly, and with the Snu114 GTPase that regulates Brr2 activity. Prp8 consists of a phylogenetically conserved Rnase H fold along with Prp8-specific elements. The function of this domain is to help assemble and stabilise the spliceosomal catalytic core and coordinate the activities of other splicing factors [
]. The overall structure of Rnase H is reminiscent of a left-hand mitten, in which a central six-stranded mixed β-sheet and the surrounding α-helices of the N-terminal domain correspond to the palm, an extended β-hairpin of the N-terminal domain comprises the thumb and the α-helical C-terminal domain represents the fingers []. This entry represents the palm region of the Rnase H domain which also includes the β-hairpin thumb.
This is the N-terminal domain found in trehalose-6-phosphate phosphatase (T6PP,
) from parasitic nematodes such as Brugia malayi. In the model nematode Caenorhabditis elegans, T6PP is essential for survival due to the toxic effect(s) of the accumulation of trehalose 6-phosphate. T6PP has also been shown to be essential in Mycobacterium tuberculosis. The N-terminal domain composed of a three-helix bundle is similar in topology to the Microtubule Interacting and Transport (MIT) domains of the Vps4-like ATPases from Sulfolobus acidocaldarius. MIT domains are protein-interacting domains typically associated with multivesicular body formation, cytokinetic abscission, or viral budding. Mutational analysis indicate that deletion or mutation of the MIT-like domain is highly destabilizing to the enzyme [
].This helical bundle domain is also found towards the C terminus in TPS-1 and TPS-2 (trehalose phosphate synthase) from C. elegans, which otherwise show little similarity to T6PP in their N-terminal halves, corresponding to the catalytic domains [
].
This entry represents the Dpy-19 protein from Caenorhabditis elegans and its homologues in other Metazoa, including mammals. In C. elegans, Dpy-19 is required to orient neuroblasts QL and QR correctly on the anterior/posterior (A/P) axis. These neuroblasts are born in the same A/P position, but polarise and migrate left/right asymmetrically, where QL migrates toward the posterior and QR migrates toward the anterior. After their migrations, QL (but not QR) switches on the Hox gene mab-5. Dpy-19 is required along with Unc-40 to express Mab-5 correctly in the Q cell descendants [
]. A mammalian dpy-19 homologue was found to be expressed in GABAergic neurons [
]. The mammalian homologue of Mab-5 is the Gsh2 homeobox transcription factor, which plays a crucial role in the development of GABAergic neurons. Dpy-19 has been shown recently to be a C-mannosyltransferase that mediates C-mannosylation of tryptophan residues [
].
In eukaryotes and archaea, the e/aIF2 factor is involved in the initiation of protein biosynthesis. In its GTP bound form, e/aIF2 delivers methionylated initiator tRNA to the small subunit of the ribosome. After the pairing between the AUG initiation codon on mRNA and the CAU anticodon of the initiator tRNA, GTP is hydrolysed and e/aIF2:GDP is released from the ribosome. In eukaryotes, eIF2B acts as the guanine nucleotide exchange factor for eIF2. Archaea have no equivalent of eIF2B, and the exchange between GDP and GTP is thought to be spontaneous [
]. eIF2 is composed of three subunits, alpha, beta and gamma. The gamma subunit forms the core of the heterotrimer and confers both tRNA binding and GTP/GDP binding [].This entry represents the domain 2 of eIF2gamma (EIF2g) from eukaryota and archaea. It adopts a β-barrel structure, and is involved in binding to both charged tRNA [
].
T-lymphoma invasion and metastasis-inducing protein 1 (Tiam1) is a guanine exchange factor (GEF) for CDC42 and the Rho-family GTPase Rac1, which plays an important role in cell-matrix adhesion and in cell migration [
,
]. Tiam1 is involved in multiple steps of tumorigenesis [].Tiam2 has been shown to localise to the nuclear envelope and to regulate Rac1 activity at the nuclear envelope which regulates the perinuclear actin cap [
]. It has been shown to promote invasion and motility of non-small cell lung cancer cells []. It has also been shown to promote epithelial-to-mesenchymal transition and results in proliferation and invasion in liver cancer cells []. This entry includes a group of guanine nucleotide exchange factors, including Tiam1/2 from humans and Sif from Drosophila [
,
,
]. Tiam1/2 are activators of the Rho GTPase Rac1 and critical for cell morphology, adhesion, migration, and polarity [].
Glycerol enters bacterial cells via facilitated diffusion, an energy-independent transport process catalysed by the glycerol transport facilitator GlpF, an integral membrane protein of the aquaporin family. Intracellular glycerol is usually converted to glycerol-3-P in an ATP-requiring phosphorylation reaction catalysed by glycerol kinase (GlpK). Glycerol-3-P, the inducer of the glpFK operon, is not a substrate for GlpF and hence remains entrapped in the cell where it is metabolized further. In some bacterial species, for example Bacillus firmus, glycerol-3-P activates the antiterminator GlpP [
]. In B. subtilis, glpF and glpK are organised in an operon followed by the glycerol-3-P dehydrogenase-encoding glpD gene and preceded by glpP coding for an antiterminator regulating the expression of glpFK, glpD and glpTQ. Their induction requires the inducer glycerol-3-P, which activates the antiterminator GlpP by allowing it to bind to the leader region of glpD and presumably also of glpFK and glpTQ mRNAs.
Ammonia monooxygenase/particulate methane monooxygenase, subunit C
Type:
Family
Description:
Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related [
]. These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules []. These enzymes are composed of 3 subunits - A (), B (
) and C (
) - and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain[
].The C subunit from Methylococcus capsulatus str. Bath resides primarily in the membrane and consists of five transmembrane helices. Several conserved residues contribute to a metal binding centre [
].
Ammonia monooxygenase/particulate methane monooxygenase, subunit B
Type:
Family
Description:
Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related [
]. These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules []. These enzymes are composed of 3 subunits - A (), B (
) and C (
) - and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain[
].The soluble regions of these enzymes derive primarily from the B subunit. This subunit forms two antiparallel β-barrel-like structures and contains the mono- and di- nuclear copper metal centres [
].
Phosphoinositide-specific phospholipase C (PI-PLC), also known as 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase, plays a role in the inositol phospholipid signaling by hydrolysing phosphatidylinositol-4,5-bisphosphate to produce the second messengers inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). These cause the increase of intracellular calcium concentration and the activation of protein kinase C (PKC), respectively.The PLC family in murine or human species is comprised of multiple subtypes. On the basis of their structure, they have been divided into five classes, beta (beta-1, 2, 3 and 4), gamma (gamma-1 and 2), delta (delta-1, 3 and 4), epsilon, zeta, and eta types [
,
].The PLC-eta gene is transcribed to several splicing variants. This entry represents PLC-eta-1, which may have an important role in the brain [
,
].This entry represents the catalytic domain of PLC-eta1, a TIM barrel with two highly conserved regions (X,
, and Y,
) split by a highly degenerate linker sequence [
].
Hermansky-Pudlak syndrome (HPS) is a disorder of organelle biogenesis in which oculocutaneous albinism, bleeding and pulmonary fibrosis result from defects of melanosomes, platelet dense granules and lysosomes [
]. HPS is common in Puerto Rico, where is mostly caused by mutations in the genes HPS1 or HPS3. Another HPS locus, HPS4 was identified by using mouse models []. It was suggested that HPS4 and HPS1 proteins may function in the same pathway of organelle biogenesis [].This family represents BLOC-3 complex member HPS4, a component of the BLOC-3 complex, a complex that acts as a guanine exchange factor (GEF) for RAB32 and RAB38, promotes the exchange of GDP to GTP, converting them from an inactive GDP-bound form into an active GTP-bound form. The BLOC-3 complex plays an important role in the control of melanin production and melanosome biogenesis and promotes the membrane localization of RAB32 and RAB38 [
].
Glutamyl-tRNA(Gln) amidotransferase (Gat;
) provides a means of producing correctly charged Gln-tRNA(Gln) through the transamidation of mis-acylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase [
,
]. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The enzyme is composed of three subunits: A (an amidase), B and C. It also exists in eukaryotes as a protein targeted to the mitochondria.The heterotrimer GatABC is involved in converting Glu to Gln and/or Asp to Asn, when the amino acid is attached to the appropriate tRNA. In Lactobacillus, GatABC is responsible for producing tRNA(Gln). In Archaea, GatABC is responsible for producing tRNA(Asn), while GatDE is responsible for producing tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyses both tRNA(Gln) and tRNA(Asn).This entry represents the first α-helical subdomain found in the C-terminal structural domain of GatB and GatE subunits.
Phage integrases are enzymes that mediate unidirectional site-specific recombination between two DNA recognition sequences, the phage attachment site, attP, and the bacterial attachment site, attB [
]. Integrases may be grouped into two major families, the tyrosine recombinases and the serine recombinases, based on their mode of catalysis. Tyrosine family integrases, such as Bacteriophage lambda integrase, utilise a catalytic tyrosine to mediate strand cleavage, tend to recognise longer attP sequences, and require other proteins encoded by the phage or the host bacteria.The recombinases Cre from phage P1, XerD from Escherichia coli and Flp from yeast are members of the tyrosine recombinase family, and have a two-domain motif resembling that of lambda integrase, as well as sharing a conserved binding mechanism []. The structural fold of their catalytic core domains resemble that of Lambda integraseThis entry contains XerD-like putative tyrosine recombinases from the Streptococcaceae family.
This entry includes the C subunit of the bacterial/archaeal aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferases (known as GatC) and eukaryotic Glu-tRNAGln amidotransferases.Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase ([intenz:6.3.5.-]) allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) []. The enzyme is composed of three subunits: A (an amidase), B and C. It also exists in eukaryotes as a protein targeted to the mitochondria.The heterotrimer GatABC is involved in converting Glu to Gln and/or Asp to Asn, when the amino acid is attached to the appropriate tRNA. In Lactobacillus, GatABC is responsible for producing tRNA(Gln). In Archaea, GatABC is responsible for producing tRNA(Asn), while GatDE is responsible for producing tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyses both tRNA(Gln) and tRNA(Asn).
Helicobacter pylori is a prevalent bacterial, gastroduodenal pathogen of humans that can express Lewis (Le) and related antigens in the O-chains of its surface lipopolysaccharide. The alpha1,3-fucosyltransferase VI (FUT VI) protein is a key enzyme for synthesis of sialyl Lewis X and Lewis X in epithelial cells [
]. Despite striking functional similarity, there is low sequence homology between the bacterial and mammalian alpha(1,3/4)- and alpha(1,2)-fucosyltransferases. Le antigen expression and fucosylation have multiple biological effects on pathogenesis and disease outcome of H. pylori [
]. The sialyl-Lewis X (SLe(x)) determinant is important in leukocyte extravasation, metastasis and bacterial adhesion []. Changes in enzyme activity and the expression levels of alpha(1,6)fucosyltransferase [alpha(1,6)FT]occur in certain types of malignant transformations. Alpha(1,6)FT activity is higher in tumour tissue than in healthy tissue. Increased alpha(1,6)FT expression is also found in tumour tissues as compared to healthy and transitional tissues, inflammatory lesions and adenomas [
].This group represents an alpha-(1,3)-fucosyltransferase/alpha-(1,4)-fucosyltransferase found in plants.
The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1 to Not5), Caf1, Caf40, Caf130 and Ccr4 [
]. The Ccr4-Not complex regulates many differentcellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress [
]. Caf1 and Ccr4, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1, a putative RNA helicase thought to be a component of the decapping complex []. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase [].The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [
].
NADH:ubiquinone oxidoreductase (complex I) (
) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) [
]. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondria, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins [].This entry contains members of the complex I subunit 4 family. Members of this family include the 13th structural gene, M, of bacterial NADH dehydrogenase I (based on Escherichia coli), as well as chain 4 of the corresponding mitochondrial complex I and of the chloroplast NAD(P)H dehydrogenase complex.
This family of sequences describe farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologues lack the C-terminal predicted transmembrane region universally conserved among members of this family and therefore are not included in this group. These enzymes catalyse the formation of squalene by the reductive dimerisation of two farnesyl diphosphate molecules in a two-step reaction. This reaction occurs at the final branch point of the isoprenoid biosynthesis pathway, and is the first committed step in cholesterol biosynthesis.2 farnesyl diphosphate --->presqualene diphosphate --->squalene The human enzyme (
) is a membrane-bound monomer which folds as a single domain [
].This family also includes squalene synthase-like (SSL) proteins from green algae. SSL-3 (Botryococcene synthase) produces botryococcene when coexpressed with SSL-1 (Presqualene diphosphate synthase). SSL-3 has no activity with farnesyl diphosphate as substrate [
]. SSL-2 (Botryococcus squalene synthase) produces squalene when coexpressed with SSL-1 and bisfarnesyl ether [].
This enzyme catalyzes the key, penultimate step in biosynthesis of trehalose, a compatible solute made as an osmoprotectant in some species in all three domains of life. The gene symbol OtsA stands for osmotically regulated trehalose synthesis A. Trehalose helps protect against both osmotic and thermal stresses, and is made from two glucose subunits. This entry excludes glucosylglycerol-phosphate synthase, an enzyme of an analogous osmoprotectant system in many cyanobacterial strains. This entry does not identify archaeal examples, as they are more divergent than glucosylglycerol-phosphate synthase. Sequences that score in the gray zone between the trusted and noise cut offs include a number of yeast multidomain proteins in which the N-terminal domain may be functionally equivalent to this family. The gray zone also includes the OtsA of Cornyebacterium glutamicum (and related species), shown to be responsible for synthesis of only trace amounts of trehalose while the majority is synthesized by the TreYZ pathway; the significance of OtsA in this species is unclear (see [
]).
Coa1 is an inner mitochondrial membrane protein that associates with Shy1 and is required for cytochrome oxidase complex IV assembly. It contains a conserved hydrophobic segment (amino acids 74-92) with the potential to form a membrane-spanning helix. The N terminus of Coa1 is rich in positively charged amino acids and could form an amphipathic alpha helix, characteristic of a mitochondrial presequence. A cleavage site for the mitochondrial processing peptidase is predicted adjacent to the presequence. Upon in vitro import into mitochondria, Coa1 is processed to a mature form, indicating that it possesses a cleavable presequence [
]. The eukaryotic cytochrome oxidase complex consists of 12-13 subunits, with three mitochondrial encoded subunits, Cox1-Cox3, forming the core enzyme. Translation of the Cox1 transcript requires the two promoters, Pet309 and Mss51, and the latter has an additional role in translational elongation. Coa1 is necessary for linking the activity of Mss51 to Cox1 insertion into the assembly complex [].
Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function [
]. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Inosine-uridine preferring nucleoside hydrolase (
) (IU-nucleoside hydrolase or IUNH) is an enzyme first identified in protozoan [
] that catalyses the hydrolysis of all of the commonly occuring purine and pyrimidine nucleosides into ribose and the associated base, but has a preference for inosine and uridine as substrates. This enzyme is important for these parasitic organisms, which are deficient in de novosynthesis of purines, to salvage the host purine nucleosides. IUNH from Crithidia fasciculata has been sequenced and characterised, it is an homotetrameric enzyme of subunits of 34 Kd. An histidine has been shown to be important for the catalytic mechanism, it acts as a proton donor to activate the hypoxanthine leaving group.
A highly conserved region located in the N-terminal extremity contains four conserved aspartates that have been shown [
] to be located in the active site cavity.IUNH is evolutionary related to a number of uncharacterised proteins from various biological sources.This entry represents the structural domain of IUNH.
Inosine-uridine preferring nucleoside hydrolase (
) (IU-nucleoside hydrolase or IUNH) is an enzyme first identified in protozoan [
] that catalyses the hydrolysis of all of the commonly occuring purine and pyrimidine nucleosides into ribose and the associated base, but has a preference for inosine and uridine as substrates. This enzyme is important for these parasitic organisms, which are deficient in de novosynthesis of purines, to salvage the host purine nucleosides. IUNH from Crithidia fasciculata has been sequenced and characterised, it is an homotetrameric enzyme of subunits of 34 Kd. An histidine has been shown to be important for the catalytic mechanism, it acts as a proton donor to activate the hypoxanthine leaving group.
A highly conserved region located in the N-terminal extremity contains four conserved aspartates that have been shown [
] to be located in the active site cavity.IUNH is evolutionary related to a number of uncharacterised proteins from various biological sources.
Tryptophan synthase (
) catalyzes the last step in the biosynthesis of tryptophan [
,
]:L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O
It has two functional domains, each found in bacteria and plants on a separate subunit. In Escherichia coli, the two subunits, A and B, are encoded by the trpA and trpB genes respectively. The alpha chain is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and the beta chain is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together in a single multifunctional protein, in the order: (NH2-A-B-COOH) [
,
]. The two domains of the Neurospora crassa polypeptide are linked by a connector of 54-amino acid residues that has less than 25% identity to the 45-residue connector of the Saccharomyces cerevisiae (Baker's yeast) polypeptide. Two acidic residues are believed to serve as proton donors/acceptors in the enzyme's catalytic mechanism.
C-5 cytosine-specific DNA methylases (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA [
,
,
]. Such enzymes are found in the proteins described below.As a component of type II restriction-modification systems in prokaryotes and some bacteriophages. Such enzymes recognise a specific DNA sequence where they methylate a cytosine. In doing so, they protect DNA from cleavage by type II restriction enzymes that recognise the same sequence. The sequences of a large number of type II C-5 Mtases are known. In vertebrates, there are a number of C-5 Mtases that methylate CpG dinucleotides. The sequence of the mammalian enzyme is known. C-5 Mtases share a number of short conserved regions. This conserved region contains a conserved Pro-Cys dipeptide in which the cysteine has been shown to be involved in the catalytic mechanism; it appears to form a covalent intermediate with the C6 position of cytosine [
].
This entry represents the 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase family. Proteins in this family include deaminase, D-cysteine desulfhydrase, phenylserine dehydratase and L-cysteate sulfo-lyase. 1-aminocyclopropane-1-carboxylate deaminase (
) catalyses a cyclopropane ring-opening reaction, the irreversible conversion of 1-aminocyclopropane-1-carboxylate (ACC) to ammonia and alpha-ketobutyrate [
]. Some plant growth-promoting rhizobacteria can produce 1-aminocyclopropane-1-carboxylate deaminase to enhance plant growth [,
]. D-cysteine desulfhydrase (d-CDes) (
) catalyses the alpha, beta-elimination reaction of D-cysteine and of several D-cysteine derivatives. The Escherichia coli d-CDes catalyses D-cysteine into pyruvate, H2S, and NH3 [
,
,
]. The physiological function of bacterial d-CDes is not clear. L-cysteate sulfo-lyase (
) catalyses the desulfonation and deamination of L-cysteate, yielding pyruvate, sulphite and ammonium. It is involved in a L-cysteate degradation pathway that allows Silicibacter pomeroyi to grow on L-cysteate as the sole source of carbon and energy. To a lesser extent, it can also act on D-cysteine in vitro, leading to the production of pyruvate, sulfide and ammonium [
].
This entry represents the ABCE family of ATP-binding cassette (ABC) transporters and solely comprises of the ABCE1 gene product (also known as RNase L inhibitor, RLI1) [
,
,
]. RLI1 contains 2 nucleotide-binding domains (NBDs) typical of the ABC transporter protein superfamily []; however, it lacks the transmembrane domains required for membrane transport functions [,
]. RLI1 was first identified as an endoribonuclease inhibitor that interacts directly with RNase L to prevent it from binding 2-5A (5'-phosphorylated 2',5'-linked oligo- adenylates) []. RNase L plays a major role in the anti-viral and anti-proliferative activities of interferons, and its inhibition by RLI1 occurs in a concentration-dependent manner [,
]. Recently, RLI1 has been shown to be essential for the assembly of immature HIV-1 capsids in insect cells and higher eukaryotic cell types []. RLI1 expression is induced during HIV type I infection, and is understood to bind HIV-1 Gag (p55) polypeptides following their translation, and to promote their assembly into immature HIV-1 capsids [,
,
].
This domain is found mainly in proteins from phages and type II, type III and type IV secretion systems [
,
,
,
].Bacterial lytic transglycosylases degrade murein via cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine, with the concomitant formation of a 1,6-anhydrobond in the muramic acid residue. There are both soluble (Slt enzymes) and membrane-bound (Mlt enzymes) lytic transglycosylases that differ in size, sequence, activity, specificity and location. The multi-domain structure of the 70 Kd soluble lytic transglycosylase Slt70 is known [
]. Slt70 has 3 distinct domains, each rich in alpha helices: an N-terminal superhelical U-shaped domain, a superhelical linker domain (L-domain, ), and a C-terminal catalytic domain (
). Both the U- and L-domain share a similar superhelical structure. These two domains are connected, and together form a closed ring with a large central hole; the catalytic domain is packed on top of, and interacts with, this ring. The catalytic domain has a lysosome-like fold.
Sucrose occupies a central position in the metabolic pathways of all plants and plays a variety of roles including transport sugar, storage reserve, compatible solute, and signal compound [
]. This compound is produced by the combined action of two enzymes, sucrose-phosphate synthase () and sucrose-phosphate phosphatase (
), via the intermediate sucrose 6-phosphate. Several studies have shown a positive correlation between sucrose-phosphate synthase activity and plant growth rate and yield in agronomically important plants, though direct proof of a causal link is lacking.
This entry represents sucrose-phosphate synthase from plants, which is known to exist in multigene families in several species of both monocots and dicots. The enzyme contains an N-terminal domain glucosyltransferase domain, a variable linker region, and a C-terminal domain similar to that of sucrose-phosphate phosphatase, the next and final enzyme of sucrose biosynthesis. The C-terminal domain is likely to serve a binding - not a catalytic - function, as sucrose-phosphate phosphatase is always encoded by a distinct protein.
Inositol phosphates (IPs) act as signalling messengers to regulate various cellular processes such as growth. This entry includes a group of inositol polyphosphate kinase, including inositol polyphosphate multikinase Arg82 and Inositol hexakisphosphate/inositol heptakisphosphate kinase Kcs1 from budding yeast. They play important roles in vacuole biogenesis and the cell's response to certain environmental stresses. The kinase activity of Arg82 and Kcs1 is required for the production of soluble inositol phosphates [
]. Independently of its catalytic activity, Arg82 is crucial for assembling the Arg80-Mcm1 protein complex at the promoter region of genes involved in arginine metabolism [].This entry also includes human inositol hexakisphosphate kinase 1/2/3 (IP6K1/2/3)[
], inositol polyphosphate multikinase (IPMK) [] and inositol-trisphosphate 3-kinase A/B/C (IP3KA/B/C) []. They are involved in inositol phosphate biosynthesis []. Independently of its catalytic activity, IPMK mediates the activation of mammalian target of rapamycin (mTOR) in response to essential amino acids [. Crystallographic analysis showed that the disordered domains of IPMK modulates its kinase activity [
].
In prokaryotes, undecaprenyl diphosphate synthase (UPP synthase, di-trans-poly-cis-decaprenylcistransferase or ditrans,polycis-undecaprenyl-diphosphate synthase (
)), catalyzes the formation of the carrier lipid undecaprenyl pyrophosphate (UPP) in bacterial cell wall peptidoglycan biosynthesis from isopentenyl pyrophosphate (IPP) [
,
,
,
,
,
,
,
,
,
,
,
,
,
]. Cis (Z)-Isoprenyl diphosphate synthase (cis-IPPS) catalyzes the successive 1'-4 condensation of the IPP molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. cis-IPPS form homodimers and are mechanistically and structurally distinct from trans-IPPS, which lack the DDXXD motifs, yet require Mg2+for activity. Homologues are also found in archaebacteria and include a number of uncharacterised proteins including some from yeasts.
This entry also matches related enzymes that transfer alkyl groups, such as dehydrodolichyl diphosphate synthase from eukaryotes, which catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate.
This entry represents tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit Trm82 and its homologues, wuho from flies and WDR4 from humans. In Saccharomyces cerevisiae, Trm82 is the non-catalytic subunit of the tRNA methyltransferase complex which consists of Trm8 and Trm82 [
,
]. It is essential for the enzyme activity and may function in regulating the the Trm8 protein []. In humans, WDR4 forms the tRNA methyltransferase complex with METTL1 (Trm8 homologue). It is required to stabilise and induce conformational changes of the catalytic subunit METTL1 [
]. It is required for the formation of N7-methylguanine at position 46 (m7G46) in tRNA [,
] and also for the formation of N7-methylguanine at internal sites in a subset of mRNAs []. WDR4 is also involved in the methylation of a specific subset of miRNAs, such as let-7 []. Independently of METTL1, it also plays a role in genome stability: localizes at the DNA replication site and regulates endonucleolytic activities of FEN1 [].
Uricase (
) (urate oxidase) [
] is the peroxisomal enzyme responsiblefor the degradation of urate into allantoin:
Urate + O2+ H
2O = 5-hydroxyisourate + H
2O
2Some species, like primates and birds, have lost the gene for uricase and are therefore unable to degrade urate []. Uricase is a protein of 300 to 400 amino acids, its sequence is well conserved.It is mainly localised in the liver, where it forms a large electron-dense paracrystalline core in many peroxisomes [
].The enzyme exists as a tetramer of identical subunits,
each containing a possible type 2 copper-binding site []. In legumes, 2 forms of uricase are found: in the roots, the tetrameric form; and, in the uninfected cells of root nodules, a monomeric form, which plays animportant role in nitrogen-fixation [
].The signature pattern used to create this entry covers a highly conserved region located in the central part of the sequence.
This group represents alpha-hydroxy acid FMN-dependent dehydrogenases, including human glycolate oxidase (GO), L-lactate oxidase (LOX) [
] and bacterial L-lactate dehydrogenase. GO catalyses the FMN-dependent oxidation of glycolate to glyoxylate and glyoxylate to oxalate. The latter is a key metabolite in kidney stone formation. 4-carboxy-5-dodecylsulphanyl-1,2,3-triazole (CDST) is an inhibitor of this enzyme. In contrast to most alpha-hydroxy acid oxidases, including spinach glycolate oxidase, a loop region, known as loop 4, is completely visible when the GO active site contains a small ligand. Since this is an unique structural feature, it has the potential to be a target for drugs to decrease glycolate and glyoxylate levels in primary hyperoxaluria type 1 patients who have the inability to convert peroxisomal glyoxylate to glycine [].This entry also includes the fungal protein FUB9 by virtue of sequence similarity to the FMN-dependent alpha-hydroxy acid dehydrogenase family. FUB9 is an oxidase that is part of the gene cluster that mediates the biosynthesis of fusaric acid [
].
UDP-3-O-N-acetylglucosamine deacetylases are zinc-dependent metalloamidases that catalyse the second and committed step in the biosynthesis of lipid A. Lipid A anchors lipopolysaccharide (the major constituent of the outer membrane) into the membrane in Gram-negative bacteria. LpxC shows no homology to mammalian metalloamidases and is essential for cell viability, making it an important target for the development of novel antibacterial compounds [
]. The structure of UDP-3-O-N-acetylglucosamine deacetylase (LpxC) from Aquifex aeolicus has a two-layer alpha/beta structure similar to that of the second domain of ribosomal protein S5, only in LpxC there is a duplication giving two structural repeats of this fold, each repeat being elaborated with additional structures forming the active site. LpxC contains a zinc-binding motif, which resides at the base of an active site cleft and adjacent to a hydrophobic tunnel occupied by a fatty acid []. This tunnel accounts for the specificity of LpxC toward substrates and inhibitors bearing appropriately positioned 3-O-fatty acid substituents []. This superfamily represents the C-terminal domain.
Acylphosphatase (
) is an enzyme of approximately 98 amino acid residues that specifically catalyses the hydrolysis of the carboxyl-phosphate bond of acylphosphates [
], its substrates including 1,3-diphosphoglycerate and carbamyl phosphate []. The enzyme has a mainly β-sheet structure with 2 short α-helical segments. It is distributed in a tissue-specific manner in a wide variety of species, although its physiological role is as yet unknown []: it may, however, play a part in the regulation of the glycolytic pathway and pyrimidine biosynthesis []. There are two known isozymes. One seems to be specific to muscular tissues, the other, called 'organ-common type', is found in many different tissues. A number of bacterial and archebacterial hypothetical proteins are highly similar to that enzyme and that probably possess the same activity. This entry represents a conserved site found in the acylphosphatase domain. It is also found in an acylphosphatase-like domain in some prokaryotic hydrogenase maturation HypF carbamoyltransferases [
,
].
This entry represents a group of ubiquitin-like-conjugating enzymes, including Atg3 and Atg10.Atg3 is the E2 enzyme for the LC3 lipidation process [
]. It is essential for autophagocytosis. The super protein complex, the Atg16L complex, consists of multiple Atg12-Atg5 conjugates. Atg16L has an E3-like role in the LC3 lipidation reaction. The activated intermediate, LC3-Atg3 (E2), is recruited to the site where the lipidation takes place []. Atg3 catalyses the conjugation of Atg8 and phosphatidylethanolamine (PE). Atg3 has an α/β-fold, and its core region is topologically similar to canonical E2 enzymes. Atg3 has two regions inserted in the core region and another with a long α-helical structure that protrudes from the core region as far as 30 A [
]. It interacts with Atg8 through an intermediate thioester bond between Cys-288 and the C-terminal Gly of Atg8. It also interacts with the C-terminal region of the E1-like Atg7 enzyme.Atg10 acts as an E2-like enzyme that catalyzes the conjugation of ATG12 to ATG5 [].
cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small β-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs [
]. In cEGFs the C-terminal thiol resides on the C-terminal β-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue.
Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [
] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNAreplication [
]. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta.Homologues of PCNA have also been identified in the archaea (known as DNA polymerase sliding clamp) [
,
] and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. The N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA [
].
Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [
] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNAreplication [
]. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta.Homologues of PCNA have also been identified in the archaea (known as DNA polymerase sliding clamp) [
,
] and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. The N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA [
].
This entry represents HAUS augmin-like complex subunit 2 from animals (HAUS2) and plants (AUG2) [
,
]. The HAUS (Homologous to AUgmin Subunits) individual subunits have been designated HAUS1 to HAUS8 [
]. In animals, HAUS augmin-like complex subunit 2 is a component of the HAUS augmin-like complex, which localises to the centrosomes and interacts with the gamma-tubulin ring complex (gamma-TuRC) []. The interaction between augmin and gamm-TuRC is important for spindle microtubule generation and affects the mitotic progression and cytokinesis []. HAUS2 may also increase the tension between spindle and kinetochore allowing for chromosome segregation during mitosis []. The HAUS augmin-like complex subunit 2 was previously known as centrosomal protein of 27kDa (Cep27).In plants, the augmin complex contains 8 subunits, including two plant-specific subunits [
]. Despite lacking cetrosomes, the augmin complex in plants plays an important part in gamma-tubulin-dependent MT nucleation and the assembly of microtubule arrays during mitosis [].
NADH:ubiquinone oxidoreductase (complex I) (
) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) [
]. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondria, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins [].This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes.
This entry represents the sugar isomerase enzymes ribose 5-phosphate isomerase B (RpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB). Galactose-6-phosphate isomerase (
) is a heteromultimeric protein consisting of subunits LacA and LacB, and catalyses the conversion of D-galactose 6-phosphate to D-tagatose and 6-phosphate in the tagatose 6-phosphate pathway of lactose catabolism [
]. Galactose-6-phosphate isomerase is induced by galactose or lactose.Ribose 5-phosphate isomerase (
) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type alpha/beta/alpha sandwich topology [
].
This entry is most closely related to the 3-isopropylmalate dehydratase
. It includes methanogen homoaconitase small subunit HacB from Methanocaldococcus jannaschii [
,
], 3-isopropylmalate dehydratase small subunit LeuD from Salmonella typhimurium [], 2,3-dimethylmalate dehydratase small subunit DmdB from Eubacterium barkeri [] and AM-toxin AMT8, an aconitase, from Alternaria alternata []. The structure of the Pyrococcus horikoshii small subunit (
) has recently been determined [
]. As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.
Histidinol dehydrogenase (HDH) catalyses the terminal step in the biosynthesis of histidine in bacteria, fungi, and plants, the four-electron oxidation of L-histidinol to histidine.In 4-electron dehydrogenases, a single active site catalyses 2 separate oxidation steps: oxidation of the substrate alcohol to an intermediate aldehyde; and oxidation of the aldehyde to the product acid, in this case His [
]. The reaction proceeds via a tightly- or covalently-bound inter-mediate, and requires the presence of 2 NAD molecules []. By contrast with most dehydrogenases, the substrate is bound before the NAD coenzyme []. A Cys residue has been implicated in the catalytic mechanism of the second oxidative step [].In bacteria HDH is a single chain polypeptide; in fungi it is the C-terminal domain of a multifunctional enzyme which catalyses three different steps of histidine biosynthesis; and in plants it is expressed as nuclear encoded protein precursor which is exported to the chloroplast [
].
Histidinol dehydrogenase (
) (HDH) catalyses the terminal step in the biosynthesis of histidine in bacteria, fungi, and plants, the four-electron oxidation of L-histidinol to histidine.
In 4-electron dehydrogenases, a single active site catalyses 2 separate oxidation steps: oxidation of the substrate alcohol to an intermediate aldehyde; and oxidation of the aldehyde to the product acid, in this case His [
]. The reaction proceeds via a tightly- or covalently-bound inter-mediate, and requires the presence of 2 NAD molecules []. By contrast with most dehydrogenases, the substrate is bound before the NAD coenzyme []. A Cys residue has been implicated in the catalytic mechanism of the second oxidative step [].In bacteria HDH is a single chain polypeptide; in fungi it is the C-terminal domain of a multifunctional enzyme which catalyzes three different steps of histidine biosynthesis; and in plants it is expressed as nuclear encoded protein precursor which is exported to the chloroplast [
].
Histidinol dehydrogenase (HDH) catalyses the terminal step in the biosynthesis of histidine in bacteria, fungi, and plants, the four-electron oxidation of L-histidinol to histidine.In 4-electron dehydrogenases, a single active site catalyses 2 separate oxidation steps: oxidation of the substrate alcohol to an intermediate aldehyde; and oxidation of the aldehyde to the product acid, in this case His [
]. The reaction proceeds via a tightly- or covalently-bound inter-mediate, and requires the presence of 2 NAD molecules []. By contrast with most dehydrogenases, the substrate is bound before the NAD coenzyme []. A Cys residue has been implicated in the catalytic mechanism of the second oxidative step [].In bacteria HDH is a single chain polypeptide; in fungi it is the C-terminal domain of a multifunctional enzyme which catalyses three different steps of histidine biosynthesis; and in plants it is expressed as nuclear encoded protein precursor which is exported to the chloroplast [
].This entry represents histidinol dehydrogenase
.
This entry represents a conserved site found towards the C-terminal of the YjgF family members. YjgF contains the enamine/imine deaminase activity and can accelerate the release of ammonia from reactive enamine/imine intermediates of the pyridoxal 5'-phosphate-dependent threonine dehydratase (IlvA). Therefore, YjgF is also known as RidA (reactive intermediate/imine deaminase A) [
]. The RidA family members are widely distributed in eubacteria, archaea and eukaryotes. Although they share protein sequences and structures similarity, they may have different functions. In this C-terminal domain, the highly conserved Arg107 of human hp14.5 (also known as ribonuclease UK114) forms salt bridges with the carboxylate oxygens of benzoate [
], while the corresponding Arg105 of Escherichia coli TdcF forms hydrogen bonds with the carboxylate oxygens of serine, threonine, and 2-oxobutanoate []. The conserved Tyr17 and Glu120 residues of E. coli TdcF have been suggested to play a role in substrate binding and positioning of a water molecule used for imine hydrolysis [].
Transferrins are eukaryotic iron-binding glycoproteins that control the level of free iron in biological fluids [
]. Evidence suggests that members of the TF family arose from the duplication and fusion of two homologous domains, with each duplicated domain binding one iron atom. Members of the family include blood serotransferrin (siderophilin); milk lactotransferrin (lactoferrin); egg white ovotransferrin (conalbumin); and membrane-associated melanotransferrin. Family members that do not bind iron have also been discovered, including inhibitor of carbonic anhydrase (ICA), which strongly binds to and inhibits certain isoforms of carbonic anhydrase [].This entry represents the transferrin-like domain, which can be further divided into two subdomains that form a cleft inside of which the iron atom is bound in iron-transporting transferrin [
]. The iron-coordinating residues consist of an aspartic acid, two tyrosines and a histidine, as well as an arginine that coordinates a requisite anion. In addition to iron and anion liganding residues, the transferrin-like domain contains conserved cysteine residues involved in disulphide bond formation.
DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks.AP endonucleases can be classified into two families based on sequence similarity. This family contains members of AP endonuclease family 1. Except for Rrp1 and arp, these enzymes are proteins of about 300 amino-acid residues. Rrp1 and arp both contain additional and unrelated sequences in their N-terminal section (about 400 residues for Rrp1 and 270 for arp). This entry represents a motif containing a glutamate residue which has been shown in the Escherichia coli enzyme to bind a divalent metal ion such as magnesium or manganese [
].
O-Glycosyl hydrolases (
) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [
,
]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.This entry represents the catalytic TIM β/α barrel common to many different families of glycosyl hydrolases found in all groups of organisms including viruses and Gene Transfer Agents (GTA) [
]. In the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) a glycosyl hydrolase domain is associated with ORFg15 (RCAP_rcc01698) [, see Fig.1, in
]. Structures have been determined for several proteins containing this glycosyl hydrolase domain, including family 13 glycosyl hydrolases (such as alpha-amylase) [
], beta-glycanases [], family 1 glycosyl hydrolases (such as beta-glucosidase) [], type II chitinases [], 1,4-beta-N-acetylmuraminidases [], and beta-N-acetylhexosaminidases [].
Subtilases [
] are an extensive family of serine proteases belonging to the MEROPS peptidase family S8 (subtilisin, clan SB). Members of this family have a catalytic triad in the order Asp, His and Ser in the sequence, which is a different order to that of families S1, S9 and S10. The catalytic activity is provided by a charge relay system similar to that of the trypsin family of serine proteases but which evolved by independent convergent evolution. The sequence around the residues involved in the catalytic triad (Asp, Ser and His) are completely different from that of the analogous residues in the trypsin serine proteases and can be used as signatures specific to that category of proteases. If a protein includes at least two of the three active site signatures, the probability of it being a serine protease from the subtilase family is 100%.This entry represents the conserved sequence around the Ser active site.
Ribokinases participate in the first step of ribose metabolism, and are members of the superfamily of carbohydrate kinases. Ribokinases phosphorylate ribose to ribose-5-phosphate in the presence of ATP and magnesium [
]:ATP + D-Ribose = ADP + D-Ribose-5-Phosphate
The phosphorylated sugar may then enter the pentose phosphate pathway [
]. There are indications that the phosphorylated sugar may also be used in the synthesis of amino acids (histidine and tryptophan). Further, links to mammalian adenosine kinase have been identified, through sequence similarity, suggesting possible homology [,
].This family also includes fructokinases [
]. Fructokinase may be involved in a sugar-sensing pathway in plants [,
].Other proteins included in this entry are: cytidine kinase from Thermococcus kodakarensis [
], Sulfofructose kinase from Escherichia coli [], Pseudouridine kinase from Arabidopsis thaliana [] and MJ0406 () from Methanocaldococcus jannaschii. MJ0406 was previously annotated as a 6-phosphofructokinases (PFK), but has since been characterised as a functional nucleoside kinase [
].
Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
Type:
Homologous_superfamily
Description:
Aminoacyl-tRNA synthetase (aaRS) is a key enzyme during protein biosynthesis. Each aaRS contains a catalytic central domain (CCD), responsible for activating amino acid, and an anticodon-binding domain (ABD), necessary for binding the anticodon in cognate tRNA. aaRSs are classified into class I and II (aaRS-I and aaRS-II) based on the topologies of CCDs. Whereas the structure of the CCDs is similar among the members of each of the two different aaRS classes, the ABDs are diverse in structure [
].The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases. Both classes of tRNA synthetases have been subdivided into three subclasses, designated Ia, Ib, Ic and IIa, IIb, IIc.This superfamily represents the anticodon binding domain (ABD) of class Ia aminoacyl-tRNA synthetases, and also matches the ABD of glycine tRNA synthetases.
The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([intenz:2.4.1.-]) and related proteins into distinct sequence based families has been described [
]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.Glycosyltransferase family 8
comprises enzymes with a number of known activities; lipopolysaccharide galactosyltransferase (
), lipopolysaccharide glucosyltransferase 1 (
), glycogenin glucosyltransferase (
), inositol 1-α-galactosyltransferase (
), α-1,3-xylosyltransferase and β-1,3-glucuronyltransferase [
]. These enzymes have a distant similarity to family GT_24.
Lectins are carbohydrate-binding proteins. Leguminous lectins form one of the largest lectin families and resemble each other in their physicochemical properties, though they differ in their carbohydrate specificities. They bind either glucose/mannose or galactose [
]. Carbohydrate-binding activity depends on the simultaneous presence of both acalcium and a transition metal ion [
]. The exact function of legume lectins is not known, but they may be involved in the attachment of nitrogen-fixing bacteria to legumes and in the protection against pathogens [,
].Some legume lectins are proteolytically processed to produce two chains, beta (which corresponds to the N-terminal) and alpha (C-terminal) [
]. The lectin concanavalin A (conA) from jack bean is exceptional in that the two chains are transposed and ligated (by formation of a new peptide bond). The N terminus of mature conA thus corresponds to that of the alpha chain and the C terminus to the beta chain []. Though the legume lectins monomer is structurally well conserved, their quaternary structures vary widely [].
This entry represents a domain with a spectrin-repeat-like fold consisting of three helices in a closed bundle with a left-handed twist. This domain is found in the succinate dehydrogenase/fumarate reductase oxidoreductase family of proteins, such as:L-aspartate oxidase (
), a flavoenzyme component of the bacterial quinolinate synthase system that catalyses the conversion of L-aspartate to oxaloacetate, the first step in the de novo biosynthesis of NAD+ [
,
].Fumarate reductase, which is part of the quinol-fumarate reductase (QFR) respiratory complex that catalyses the terminal step of anaerobic respiration when fumarate acts as the terminal electron acceptor [
].Succinate dehydrogenase (SQR;
), an iron-sulphur flavoenzyme from bacteria that is analogous to the mitochondrial respiratory complex II, forming part of the electron transport pathway from the electron acceptor (succinate) to the terminal donor (ubiquinone) [
].Adenylylsulphate reductase A subunit (
), an iron-sulphur flavoenzyme that catalyses the reversible reduction of adenosine-5'-phosphate (APS) to sulphite and AMP [
].
The ATP-grasp fold is one of several distinct ATP-binding folds, and is found in enzymes that catalyse the formation of amide bonds, catalysing the ATP-dependent ligation of a carboxylate-containing molecule to an amino or thiol group-containing molecule [
]. This fold is found in many different enzyme families, including various peptide synthetases, biotin carboxylase, synapsin, succinyl-CoA synthetase, pyruvate phosphate dikinase, and glutathione synthetase, amongst others []. These enzymes contribute predominantly to macromolecular synthesis, using ATP-hydrolysis to activate their substrates. The ATP-grasp fold shares functional and structural similarities with the PIPK (phosphatidylinositol phosphate kinase) and protein kinase superfamilies. The ATP-grasp domain consists of two subdomains with different alpha+beta folds, which grasp the ATP molecule between them. Each subdomain provides a variable loop that forms part of the active site, with regions from other domains also contributing to the active site, even though these other domains are not conserved between the various ATP-grasp enzymes [
].This entry represents subdomain 1 found at the N-terminal end of the ATP-grasp domain.
According to structural similarities and conserved sequence motifs, FAD-binding domains have been grouped in three main families: (i) the ferredoxin reductase (FR)-type FAD-binding domain, (ii) the FAD-binding domains that adopt a Rossmann fold and (iii) the p-cresol methylhydroxylase (PCMH)-type FAD-binding domain [
].The PCMH-type FAD-binding domain consists of two α-β subdomains: one is composed of three parallel β-strands (B1-B3) surrounded by α-helices, and is packed against the second subdomain containing five antiparallel β-strands (B4-B8) surrounded by α-helices [
]. The two subdomains accommodate the FAD cofactor between them []. This superfamily represents the second (C-terminal) subdomain, which is found in:CO dehydrogenase flavoprotein (N-terminal domain; [
]) family, which includes xanthine oxidase (domain 3) () [
], subunit A of xanthine dehydrogenase (domain 3) () [
], medium subunit of quinoline 2-oxidoreductase (QorM) () [
], and the beta-subunit of 4-hydroxybenzoyl-CoA reductase (HrcB) (N-terminal domain) () [
].Uridine diphospho-N-acetylenolpyruvylglucosamine reductase (MurB) (N-terminal domain) [
].
This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca
2+-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [
]. They were originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes []. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding [,
].
Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see
) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors [
]. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].This entry represents the B3 DNA binding domain. Its DNA binding activity has been demonstrated [
]. The B3 domain can be found in one or more copies.
Subtilases [
] are an extensive family of serine proteases belonging to the MEROPS peptidase family S8 (subtilisin, clan SB). Members of this family have a catalytic triad in the order Asp, His and Ser in the sequence, which is a different order to that of families S1, S9 and S10. The catalytic activity is provided by a charge relay system similar to that of the trypsin family of serine proteases but which evolved by independent convergent evolution. The sequence around the residues involved in the catalytic triad (Asp, Ser and His) are completely different from that of the analogous residues in the trypsin serine proteases and can be used as signatures specific to that category of proteases. If a protein includes at least two of the three active site signatures, the probability of it being a serine protease from the subtilase family is 100%.This entry represents the conserved sequence around the aspartic acid (Asp) active site.
Subtilases [
] are an extensive family of serine proteases belonging to the MEROPS peptidase family S8 (subtilisin, clan SB). Members of this family have a catalytic triad in the order Asp, His and Ser in the sequence, which is a different order to that of families S1, S9 and S10. The catalytic activity is provided by a charge relay system similar to that of the trypsin family of serine proteases but which evolved by independent convergent evolution. The sequence around the residues involved in the catalytic triad (Asp, Ser and His) are completely different from that of the analogous residues in the trypsin serine proteases and can be used as signatures specific to that category of proteases. If a protein includes at least two of the three active site signatures, the probability of it being a serine protease from the subtilase family is 100%.This entry represents the conserved sequence around the His active site.
The short-chain dehydrogenases/reductases family (SDR) [
,
] is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases. As the first member of this family to be characterised was Drosophila alcohol dehydrogenase, this family used to be called [,
,
] 'insect-type', or 'short-chain' alcohol dehydrogenases. Most members of this family are proteins of about 250 to 300 amino acid residues. Most dehydrogenases possess at least 2 domains [], the first binding the coenzyme, often NAD, and the second binding the substrate. This latter domain determines the substrate specificity and contains amino acids involved in catalysis. Little sequence similarity has been found in the coenzyme binding domain although there is a large degree of structural similarity, and it has therefore been suggested that the structure of dehydrogenases has arisen through gene fusion of a common ancestral coenzyme nucleotide sequence with various substrate specific domains [
].
This entry refers to the phosphoribosyl transferase (PRT) type I domain. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP). PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. This domain is found in a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase
, hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase
, ribose-phosphate pyrophosphokinase
, amidophosphoribosyltransferase
, orotate phosphoribosyltransferase
, uracil phosphoribosyltransferase
, and xanthine-guanine phosphoribosyltransferase
. In Arabidopsis, at the very N terminus of this domain is the P-Loop NTPase domain [
,
,
,
,
,
,
,
,
,
,
,
,
].
Eukaryotic pirins are highly conserved nuclear proteins that may function as transcriptional regulators with a role in apoptosis [
,
]. Prokaryotic homologues have also been identified. Both bacterial and human pirins have been shown to possess quercetinase activity [], although this is not universally true for all family members - YhaK (), for example, displays no such enzymatic activity [
].Pirin is composed of two structurally similar domains arranged face to face. Although the two domains are similar, the C-terminal domain of pirin differs from the N-terminal domain as it does not contain a metal binding site and its sequence does not contain the conserved metal-coordinating residues [
].Pirin is considered a member of the cupin superfamily on the basis of primary sequence and structural similarity. The presence of a metal binding site in the N-terminal β-barrel of pirin, may be significant in its interaction with Bcl-3 and nuclear factor I (NFI) and role in regulating NF-kappaB transcription factor activity [
].
The cryptochrome and photolyase families consist of structurally related flavin adenine dinucleotide (FAD) proteins that use the absorption of blue light to accomplish different tasks. The photolyasess use the blue light for light-driven electron transfer to repair UV-damaged DNA, while the cryptochromes are blue-light photoreceptors involved in the circadian clock for plants and animals [
,
]. On the basis of the primary structure, the cryptochrome/DNA photolyase family can be grouped into two classes []. The first class contains cryptochromes and DNA photolyases from eubacteria, archaea, fungi, animals and plants. The second class contains DNA photolyases from prokaryotes, plants and animals.Similar to the distantly related microbial class I photolyases, class 2 enzymes repair UV-induced cyclobutane pyrimidine dimer (CPD) lesions within duplex DNA using blue/near-UV light [
]. There are a number of conserved sequence regions in all known class 2 DNA photolyases, especially in the C-terminal part. The structures of the class 2 DNA photolyase from archaea and rice have been solved [,
].
This superfamily represents a structural domain found at the C-terminal of aldehyde dehydrogenases [
]. These proteins contain two similar domains, each with a 3-layer alpha/beta/alpha structure, which probably arose from a duplication; this entry covers the C-terminal a/b/a domain. These enzymes bind NAD differently from other NAD(P)-dependent oxidoreductases.
Aldehyde dehydrogenases (
and
) are enzymes that oxidize a wide variety of aliphatic and aromatic aldehydes using NADP as a cofactor. In mammals at least four different forms of the enzyme are known [
]: class-1 (or Ald C) a tetrameric cytosolic enzyme, class-2 (or Ald M) a tetrameric mitochondrial enzyme, class- 3 (or Ald D) a dimeric cytosolic enzyme, and class IV a microsomal enzyme. Aldehyde dehydrogenases have also been sequenced from fungal and bacterial species. A number of enzymes are known to be evolutionary related to aldehyde dehydrogenases. A glutamic acid and a cysteine residue have been implicated in the catalytic activity of mammalian aldehyde dehydrogenase.
Ubiquitin-activating enzyme (E1 enzyme) [
,
] activates ubiquitin by firstadenylating with ATP its C-terminal glycine residue and thereafter linking
this residue to the side chain of a cysteine residue in E1, yielding anubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is
transferred to a cysteine residue on one of the many forms of ubiquitin-conjugating enzymes (E2).
E1 is a large monomeric protein of about 110 to 115 Kd (about 1000 residues).
In yeast there are two forms (UBA1 and UBA2) [], while in plants and mammalsmultiple forms exist including a form which is Y-linked in mouse and some
other mammals and which may be involved in spermatogenesis.It has been shown that the last of the five cysteines that are conserved in the sequence of E1 from various species is the one that binds ubiquitin [
]. This entry represents a conserved region containing the second of the five conserved cysteines.
Ribulose bisphosphate carboxylase small subunit, domain
Type:
Domain
Description:
RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP), thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The small subunits induce conformational changes in the large subunits enhancing its catalytic rate. Studies in Oryza sativa demonstrate that the availability of the small subunit upregulates the transcript levels of the large subunit [
]. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [
], which results in RuBisCO being more abundant during the day when it is required.The RuBisCo small subunit consists of a central four-stranded β-sheet, with two helices packed against it [
].
FGGY carbohydrate kinases carry out ATP-dependent phosphorylation on one out of at least nine distinct sugar substrates [
]. These enzymes include L-ribulokinase () (gene araB); Erythriol kinase (
) (gene eryA); L-fucolokinase (
) (gene fucK); gluconokinase (
) (gene gntK); glycerol kinase (
) (gene glpK); xylulokinase (
) (gene xylB); L-xylulose kinase (
) (gene lyxK), D-ribulokinase (
) (gene rbtK); and rhamnulokinase (
) (gene rhaB). This family also contains a divergent subfamily functioning in quorum sensing, which phosphorylates AI-2, a bacterial signaling molecule derived from 4,5-dihydroxy-2,3-pentanedione (DPD) [
].All described members of this enzyme family are composed of two homologous actin-like ATPase domains. A catalytic cleft is formed by the interface between these two domains, where the sugar substrate and ATP co-substrate bind.This entry represents the C-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain [
,
].
FGGY carbohydrate kinases carry out ATP-dependent phosphorylation on one out of at least nine distinct sugar substrates [
]. These enzymes include L-ribulokinase () (gene araB); Erythriol kinase (
) (gene eryA); L-fucolokinase (
) (gene fucK); gluconokinase (
) (gene gntK); glycerol kinase (
) (gene glpK); xylulokinase (
) (gene xylB); L-xylulose kinase (
) (gene lyxK), D-ribulokinase (
) (gene rbtK); and rhamnulokinase (
) (gene rhaB). This family also contains a divergent subfamily functioning in quorum sensing, which phosphorylates AI-2, a bacterial signaling molecule derived from 4,5-dihydroxy-2,3-pentanedione (DPD) [
].This entry represents the N-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain [
,
].All described members of this enzyme family are composed of two homologous actin-like ATPase domains. A catalytic cleft is formed by the interface between these two domains, where the sugar substrate and ATP co-substrate bind.
This entry includes a group of methyltransferases such as leucine carboxyl methyltransferase 1 (known as Ppm1 in yeast and LCMT1 in mammals), leucine carboxyl methyltransferase 2 (Ppm2/LCMT2) and O-methyltransferase TcmP. Ppm1 regulates the activity of serine/threonine phosphatase 2A (PP2A) through methylation of the C-terminal leucine residue of the catalytic subunit of PP2A [
,
,
]. This affects the heteromultimeric composition of PP2A which in turn affects protein recognition and substrate specificity. Like many other methyltransferases Ppm1 uses S-adenosylmethionine (SAM) as the methyl donor. Ppm1 contains the common SAM-dependent methyltransferase core fold, with various insertions and additions creating a specific PP2A binding site []. Ppm2, a homologue of Ppm1, is a S-adenosyl-L-methionine-dependent methyltransferase that acts as a component of the wybutosine biosynthesis pathway, which is part of tRNA modification [].Streptomyces glaucescens TcmP is an O-methyltransferase that catalyses the methylation of the C-9 carboxy group of tetracenomycin E (TCM E) to yield TCM A2, which is then further processed to produce the antibiotic TCM C [
].
Glycyl radical enzymes are involved in a great variety of functions, including nucleotide, pyruvate and toluene metabolism [
]. A glycyl radical is formed by the removal of a hydrogen from a glycine and the resulting radical is located on the protein main chain.Escherichia coli formate C-acetyltransferase (
) is a key enzyme of anaerobic glucose metabolism; it converts pyruvate and CoA into acetyl-CoA and pyruvate. It is posttranslationally interconverted, under anaerobic conditions, from an inactive to an active form that carries a stable radical localised to a specific glycine at the C terminus [
]. Such a glycine radical is also present in E. coli (gene nrdD) [] and Bacteriophage T4 (gene nrdD or sunY) anaerobic ribonucleoside-triphosphate reductases (). In these enzymes the glycyl radical is located at the C-terminal part of the enzyme [
]. An autonomous glycyl radical cofactor also exists in Escherichia coli and bacteriophage T4 (gene grcA) [].This entry represents a domain covering the conserved region around the glycine radical.
In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. Quorum-sensing bacteria produce, release, and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. For example, enteric bacteria use quorum sensing to regulate several traits that allow them to establish and maintain infection in their host, including motility, biofilm formation, and virulence-specific genes [
]. The LuxS/AI-2 system is one of several quorum sensing mechanisms. AI-2 (autoinducer-2) is a signalling molecule that functions in interspecies communication by regulating niche-specific genes with diverse functions in various bacteria, often in response to population density. LuxS (S-ribosylhomocysteinase; ) is an autoinducer-production protein that has a metabolic function as a component of the activated methyl cycle. LuxS converts S-ribosylhomocysteine to homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD); DPD can then spontaneously cyclise to active AI-2 [
,
]. LuxS is a homodimeric iron-dependent metalloenzyme containing two identical tetrahedral metal-binding sites similar to those found in peptidases and amidases [].
Bacterial proteins GreA and GreB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as GreA or GreB, allows the resumption of elongation from the new 3' terminus [
,
]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS.
Bacterial proteins GreA and GreB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as GreA or GreB, allows the resumption of elongation from the new 3' terminus [
,
]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS.
Bacterial proteins GreA and GreB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as GreA or GreB, allows the resumption of elongation from the new 3' terminus [
,
]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS.
Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur:Recombination between inverted repeats resulting in the reversal of a DNA segment.Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment.Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation.Two unrelated families of recombinases are currently known [
]. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA , and a C-terminal helix-turn-helix DNA-binding domain.
Mrp-type antiporters comprise the cation/proton antiporter family 3 (CPA3), commonly referred to as Mrp. They are the products of operons that carry either six or seven genes (mrpA-G), and form complexes containing all subunits [
,
]. They have Na(+)/H(+) antiporter activity []. Two of the Mrp proteins, MrpA and MrpD, resemble NuoL/ND5, NuoM/ND4, NuoN/ND2, the homologous subunits that constitute the membrane-embedded, proton-translocating core of complex I [
,
,
,
]. They also resemble subunits of membrane-bound hydrogenases, such as HyfB, HyfD and HyfF from E.coli [] and F420H2 dehydrogenasa (FPO complex) subunits L, N and M [].This domain represents an N-terminal extension of
. It is found in complex I subunit NuoL/ND5, CPA3 antiporters subunit MrpA, and in F(420)H(2) dehydrogenase subunit L.
Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane.
This entry represents the polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD.The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily [
]. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) []. NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap [,
].
Angiogenic factor with G patch and FHA domains 1 (AGGF1, also known as VG5Q) functions as a potent angiogenic factor in promoting angiogenesis through interacting with TWEAK (also known as TNFSF12), which is a member of the tumour necrosis factor (TNF) superfamily that induces angiogenesis in vivo. VG5Q can bind to the surface of endothelial cells and promote cell proliferation, suggesting that it may act in an autocrine fashion. The chromosomal translocation t(5;11) and the E133K variant in VG5Q are associated with Klippel-Trenaunay syndrome (KTS), a disorder characterised by diverse effects in the vascular system. In addition to a forkhead-associated (FHA) domain and a G-patch motif, VG5Q contains an N-terminal OCtamer REpeat (OCRE) domain that is characterised by a 5-fold, imperfectly repeated octameric sequence [
,
].The OCRE (OCtamer REpeat) domain contains five repeats of an 8-residue motif, which were shown to form β-strands. Based on the architectures of proteins containing OCRE domains, a role in RNA metabolism and/or signalling has been proposed [
].
This entry includes family members such as EarP enzymes which are essential for post-translational activation of elongation factor P (EF-P). It was identified as EF-P arginine R32 specific rhamnosyl transferase in Shewanella oneidensis using dTDP-beta-L-rhamnose as donor substrate [
]. This was further confirmed for Pseudomonas aeruginosa [,
], Pseudomonas putida [] and Neisseria meningitidis []. As for S. oneidensis [] and P. aeruginosa [], EarP enzyme acts as an inverting glycosyltransferase, thus mediating the formation of an alpha-L-rhamnosidic linkage. Structural analysis show that EarP is composed of two opposing domains with Rossmann folds, thus constituting a B pattern-type glycosyltransferase (GT-B) and provide basis for arginine glycosylation by EarP []. Mutational analysis of efp and earP genes, resulted in a substantial decrease in the production of rhamnolipids and pyocyanin (important factors for colonization and invasion during infection) of P. aeruginosa. Collectively this indicates that EarP and EF-P are essential for P. aeruginosa pathogenicity []. The protein family is also annotated in the CaZy Database as GT104.
Helicobacter pylori is a prevalent bacterial, gastroduodenal pathogen of humans that can express Lewis (Le) and related antigens in the O-chains of its surface lipopolysaccharide. The alpha1,3-fucosyltransferase VI (FUT VI) protein is a key enzyme for synthesis of sialyl Lewis X and Lewis X in epithelial cells [
]. Despite striking functional similarity, there is low sequence homology between the bacterial and mammalian alpha(1,3/4)- and alpha(1,2)-fucosyltransferases. Le antigen expression and fucosylation have multiple biological effects on pathogenesis and disease outcome of H. pylori []. The sialyl-Lewis X (SLe(x)) determinant is important in leukocyte extravasation, metastasis and bacterial adhesion []. Changes in enzyme activity and the expression levels of alpha(1,6)fucosyltransferase [alpha(1,6)FT]occur in certain types of malignant transformations. Alpha(1,6)FT activity is higher in tumour tissue than in healthy tissue. Increased alpha(1,6)FT expression is also found in tumour tissues as compared to healthy and transitional tissues, inflammatory lesions and adenomas [
].This group represents an alpha-(1,3)-fucosyltransferase/alpha-(1,4)-fucosyltransferase, found in Helicobacter species.
The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([intenz:2.4.1.-]) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.Glycosyltransferase family 28
comprises enzymes with a number of known activities; 1,2-diacylglycerol 3-beta-galactosyltransferase (
); 1,2-diacylglycerol 3-beta-glucosyltransferase (
); beta-N-acetylglucosamine transferase (
).
Structural analysis suggests the C-terminal domain contains the UDP-GlcNAc binding site.This group represents a predicted family 28 glycosyltransferase, RedA.
Tumor necrosis factor (TNF) receptor associated factor 3 (TRAF3) is a highly versatile regulator that positively controls type I interferon production, but negatively regulates mitogen-activated protein (MAP) kinase activation and non-canonical nuclear factor-kB signalling [
]. It is a critical regulator of both innate and adaptive immune responses []. TRAF3 plays a role in the regulation of B-cell survival [], in the regulation of antiviral responses [], and in T-cell dependent immune responses []. It is required for normal antibody isotype switching from IgM to IgG []. Differences in the ubiquitination of TRAF3 are the key to the selective production of type I interferons versus proinflammatory cytokines [].TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded β-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors [
].
The middle and C-terminal domains of the unusual penicillin-binding protein (PBP) Tp47 have an immunoglobulin-like fold. The C-terminal domain is mainly characterised by an immunoglobulin fold with two opposing β-sheets that form the typical barrel-like structure. In contrast to the classical immunoglobulin fold, however, this has an additional β-strand inserted after strand 3. Also, the strands are connected by rather large loops. Helices are inserted between strands 2 and 3 and between strands 4 and 5. In contrast to the C-terminal domain, the middle domain contains only the characteristic seven-stranded barrel and short loops. As in domain C, a single α-helical turn is inserted between strands 2 and 3. The C-terminal domain interacts with the middle domain via a surface that has a slightly concave, goblet-like shape.Tp47 is unusual in that it displays beta-lactamase activity, and thus it does not fit the classical structural and mechanistic paradigms for PBPs, and thus Tp47 appears to represent a new class of PBP [
].
This entry represents the N-terminal ribonucleoprotein (RNP) domain of Rpa43, which is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, involved in recruiting RNAP I to the pol I promoter [
,
,
].
MatP organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle [
].This entry represents the N-terminal domain of MatP.
This family contains many uncharacterized prokaryotic polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA) [
,
]. PuuE allantoinase appears to be metal-independent and specifically catalyses the hydrolysis of (S)-allantoin into allantoic acid. Different from PuuE allantoinase, HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. Both PuuE allantoinase and HpPgdA function as homotetramers. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCA-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. In contrast to typical NodB-like DCAs, PuuE allantoinase and HpPgdA do not exhibit a solvent-accessible polysaccharide binding groove and might only bind a small molecule at the active site [,
,
].
This entry represents the C-terminal domain of H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenases. The N(5),N(10)-methylenetetrahydromethanopterin dehydrogenase system of methanogenic archaea is composed of H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd, represented by this entry) and F420-dependent methylenetetrahydromethanopterin dehydrogenase (
) [
,
]. Hmd is an iron-sulphur-cluster-free enzyme that contains an intrinsic CO ligand bound to iron []. This domain is found at the C terminus of two distinct subgroups: one has been experimentally characterised as H2-forming N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase (Hmd or HmdI), and the other one contains isozymes that have not been experimentally characterised (HmdII and HmdIII). Because all three isozyme forms are present in each of the corresponding sequenced genomes, it has been suggested that HmdII and HmdIII may not exhibit Hmd activity and may have a different biological function []. Based on on its ability to bind to aminoacyl-tRNA synthetases and tRNA, a role for HmdII has been proposed as a regulator of protein synthesis that senses intracellular methylene-H4 MPT concentration [].
Cmr2 is a subunit of a CRISPR RNA-Cas protein complex (the Cmr complex, consisting of subunits Cmr1-6), that cleaves foreign RNA in prokaryotes. Its N-terminal region is a putative HD (histidine-aspartate) nuclease domain; however, it does not participate in target RNA cleavage [
]. In fact, Cmr4 has been identified as the conserved endoribonuclease of the Cmr complex []. In Pyrococcus furiosus, the HD domain of Cmr2 is formed by eight α-helices and a β-hairpin, and lies diametrically opposite to Cmr3 [].The N-terminal domain D1 contains a ferredoxin-like fold (which contains a P-loop) and a cysteine cluster that is formed by two CXXC motifs. It is the largest of the four domains of Cmr2 and is composed of nine helices and three β-strands. ADP binds near the P-loop region of the D1 domain. The D1 domain that constitutes one face of the active site pocket might fulfil the role of fingers domain (similarly to DNA polymerases) in binding the nucleotide [
].
