Some oxygen-dependent oxidoreductases are flavoproteins that contain a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. The region around the histidine that binds the FAD group is conserved in these enzymes (see
).
The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme RimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria [
].The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see
). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [,
,
]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [
,
]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S]cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit [
].
The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see
). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [,
,
]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [
,
]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S]cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see ) [
]. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit [
].
Radical SAM domains catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [
,
].This entry represents radical SAM domains that form an alpha/beta horseshoe structure [
].
The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see
). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [,
,
]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [
,
]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S]cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see ) [
]. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit [
]. This entry represents a conserved site containing three of the conserved cysteines that form the motif in the central radical SAM fold.
The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in:
Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formationIn several other proteins associated with the translation machineryIn a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translationThe TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets [].Secondary structure prediction indicates that the TRAM domain adopts a simple β-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five β-strands in the predicted secondary structure [
].
This entry represents the C-terminal domain of 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23 [
]. Bud23 homologues can be found from yeast to human. They are S-adenosyl-L-methionine-dependent methyltransferases that specifically methylates the N7 position of a guanine in 18S rRNA []. Bud23 homologue in Arabidopsis, known as Rid2 (ROOT INITIATION DEFECTIVE 2), is also involved in pre-rRNA processing []. In humans, Bud23 is located in the Williams-Beuren syndrome (WBS) critical region [
].
This family consists of examples of the single chain form of dihydroxyacetone kinase (also called glycerone kinase) that uses ATP (
) as the phosphate donor, rather than a phosphoprotein as in Escherichia coli. This form has separable domains homologous to the K and L subunits of the E. coli enzyme, and is found in yeasts and other eukaryotes and in some bacteria, including Citrobacter freundii [
,
].The member from tomato has been shown to phosphorylate dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some other aldoses and ketoses [
]. Members from mammals have been shown to catalyse both the phosphorylation of dihydroxyacetone and the splitting of ribonucleoside diphosphate-X compounds among which FAD is the best substrate []. In yeast there are two isozymes of dihydroxyacetone kinase (Dak1 and Dak2). They are required for detoxification of dihydroxyacetone (DHA) [].
This is an fn3-like domain which is frequently found as the first of three on streptococcal C5a peptidase (SCP), a highly specific protease and adhesin/invasin [
].
An appreciable fraction of the sulphur present in mammals occurs in the form of glutathione. The synthesis of glutathione and its utilization take place by the reactions of the gamma-glutamyl cycle, which include those catalysed by gamma-glutamylcysteine and glutathione synthetases, gamma-glutamyl transpeptidase, cysteinylglycinase, gamma-glutamyl cyclotransferease, and 5-oxoprolinase [
].This domain is found in N-methylhydantoinase B, which converts hydantoin to N-carbamyl-amino acids, and in 5-oxoprolinase
which catalyses the formation of L-glutamate from 5-oxo-L-proline. These enzymes are part of the oxoprolinase family.
This domain is found in the enzymes hydantoinase A (HyuA) and oxoprolinase (
). Both enzymes catalyse reactions involving the hydrolysis of 5-membered rings via hydrolysis of their internal imide bonds [
]. This domain is also found in (4-{4-[2-(gamma-L-glutamylamino)ethyl]phenoxymethyl}furan-2-yl)methanamine synthase from
Methanocaldococcus jannaschii, which is involved in methanofuran biosynthesis, catalyzing the condensation between 5-(aminomethyl)-3-furanmethanol diphosphate and gamma-glutamyltyramine to produce 4-[N-(gamma-L-glutamyl)-p-(beta-aminoethyl)phenoxymethyl]-(aminomethyl)furan (APMF-Glu) []. D-5-(2-methylthioethyl)hydantoin amidohydrolase (HyuA) from Pseudomonasis a component of the hydantoinase process, an enzymatic cascade converting D-5-(2-methylthioethyl)hydantoin to N-carbamoyl-D-methionine [
].
This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8--delta-7 sterol isomerase), catalyses a reaction in ergosterol biosynthesis, which results in unsaturation at C-7 in the B ring of sterols [
]. Sigma 1 receptor is a low molecular mass mammalian protein located in the endoplasmic reticulum [], which interacts with endogenous steroid hormones, such as progesterone and testosterone []. It also binds the sigma ligands, which are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine []. Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA receptor function, the alpha-adrenergic system and opioid analgesia.
This domain is found at the C terminus of adenylosuccinate lyase (ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain
. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate [
].
This family consists of adenylosuccinate lyase, the enzyme that catalyzes step 8 in the purine biosynthesis pathway for de novo synthesis of IMP, and also the final reaction in the two-step sequence from IMP to AMP [
]. It is a member of lyase class I family, which functions as homotetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits [].
A number of enzymes, belonging to the lyase class, for which fumarate is a substrate, have been shown to share a short conserved sequence around a
methionine which is probably involved in the catalytic activity of this typeof enzymes [
]. The following are examples of members of this family:: 3-carboxymuconate lactonizing enzyme,
(3-carboxy-cis,cis-muconate cycloisomerase), an enzyme involved in aromatic acids catabolism [
]. : Delta-crystallin shares around 90% sequence identity with arginosuccinate lyase, showing that it is an example of a 'hijacked' enzyme - accumulated mutations have, however, rendered the protein enzymatically inactive.: Class I Fumarase enzyme,
(fumarate hydratase), which catalyses the reversible hydration of fumarate to L-malate. Class I enzymes are thermolabile dimeric enzymes (as for example: Escherichia coli fumC).
: Arginosuccinase,
(argininosuccinate lyase), which catalyses the formation of arginine and fumarate from argininosuccinate, the last step in the biosynthesis of arginine.
: Aspartate ammonia-lyase,
(aspartase), which catalyses the reversible conversion of aspartate to fumarate and ammonia. This reaction is analogous to that catalyzed by fumarase, except that ammonia rather than water is involved in the trans-elimination reaction.
: class II Fumarase enzyme,
, are thermostable and tetrameric and are found in prokaryotes (as for example: E. coli fumA and fumB) as well as in eukaryotes. The sequence of the two classes of fumarases are not closely related.
: Adenylosuccinase,
(adenylosuccinate lyase) [
], which catalyses the eighth step in the de novo biosynthesis of purines, the formation of 5'-phosphoribosyl-5-amino-4-imidazolecarboxamide and fumarate from 1-(5-phosphoribosyl)-4-(N-succino-carboxamide). That enzyme can also catalyse the formation of fumarate and AMP from adenylosuccinate. : Trans-aconitate decarboxylase 1, which decarboxylates trans-aconitate, an intermediate in the biosynthesis of itaconic acid and 2-hydroxyparaconate [
,
].
A number of enzymes, belonging to the lyase class, for which fumarate is a substrate, have been shown to share a short conserved sequence around a
methionine which is probably involved in the catalytic activity of this typeof enzymes [
]. The following are examples of members of this family:: 3-carboxymuconate lactonizing enzyme,
(3-carboxy-cis,cis-muconate cycloisomerase), an enzyme involved in aromatic acids catabolism [
]. : Delta-crystallin shares around 90% sequence identity with arginosuccinate lyase, showing that it is an example of a 'hijacked' enzyme - accumulated mutations have, however, rendered the protein enzymatically inactive.
: Class I Fumarase enzyme,
(fumarate hydratase), which catalyses the reversible hydration of fumarate to L-malate. Class I enzymes are thermolabile dimeric enzymes (as for example: Escherichia coli fumC).
: Arginosuccinase,
(argininosuccinate lyase), which catalyses the formation of arginine and fumarate from argininosuccinate, the last step in the biosynthesis of arginine.
: Aspartate ammonia-lyase,
(aspartase), which catalyses the reversible conversion of aspartate to fumarate and ammonia. This reaction is analogous to that catalyzed by fumarase, except that ammonia rather than water is involved in the trans-elimination reaction.
: class II Fumarase enzyme,
, are thermostable and tetrameric and are found in prokaryotes (as for example: E. coli fumA and fumB) as well as in eukaryotes. The sequence of the two classes of fumarases are not closely related.
: Adenylosuccinase,
(adenylosuccinate lyase) [
], which catalyses the eighth step in the de novo biosynthesis of purines, the formation of 5'-phosphoribosyl-5-amino-4-imidazolecarboxamide and fumarate from 1-(5-phosphoribosyl)-4-(N-succino-carboxamide). That enzyme can also catalyse the formation of fumarate and AMP from adenylosuccinate. : Trans-aconitate decarboxylase 1, which decarboxylates trans-aconitate, an intermediate in the biosynthesis of itaconic acid and 2-hydroxyparaconate [,
].This signature contains the conserved methionine which is probably involved in the catalytic activity.
The enzyme L-aspartate ammonia-lyase (aspartase) catalyses the reversible deamination of the amino acid L-aspartic acid, using a carbanion mechanism to produce fumaric acid and ammonium ion. Aspartases from different organisms show high sequence homology, and this homology extends to functionally related enzymes such as the class II fumarases, the argininosuccinate and adenylosuccinate lyases. The high-resolution structure of aspartase reveals a monomer that is composed of three domains oriented in an elongated S-shape [
]. The central domain, comprised of five-helices, provides the subunit contacts in the functionally active tetramer. The active sites are located in clefts between the subunits and structural and mutagenic studies have identified several of the active site functional groups. A separate regulatory site has been identified. The substrate, aspartic acid, can also play the role of an activator, binding at this site along with a required divalent metal ion.
A number of enzymes, belonging to the lyase class, for which fumarate is a substrate, have been shown to share a short conserved sequence around a methionine which is probably involved in the catalytic activity of this type of enzymes [
]. This entry represents the N-terminal region of fumarate lyase family.
Actin-binding Rho-activating protein is also known as striated muscle activator of Rho-dependent signaling (STARS) in mouse and myocyte stress 1 (MS1) in rat. STARS acts as an activator of serum response factor (SRF)-dependent transcription, possibly by inducing nuclear translocation of MKL1 or MKL2 and through a mechanism requiring Rho-actin signaling [
,
].
This domain is found both alone (in the costars family of proteins) and at the C terminus of actin-binding Rho-activating protein (ABRA). It binds to actin, and in muscle regulates the actin cytoskeleton and cell motility [
,
]. It has a winged helix-like fold consisting of three α-helices and four antiparallel beta strands. Unlike typical winged helix proteins it does not bind to DNA, but contains a hydrophobic groove which may be responsible for interaction with other proteins [].
Imidazoleglycerol-phosphate dehydratase, conserved site
Type:
Conserved_site
Description:
Imidazoleglycerol-phosphate dehydratase (IGPD;
) catalyzes the dehydration of imidazole glycerol phosphate to imidazole acetol phosphate, the sixth step of histidine biosynthesis in plants and microorganisms where the histidine is synthesized de novo. There is an internal repeat in the protein domain that is related by pseudo-dyad symmetry, perhaps as a result of an ancient gene duplication. The apo-form of IGPD exists as a catalytically inactive trimer which, in the presence of specific divalent metal cations such as manganese (Mn2+), cobalt (Co2+), cadmium (Cd2+), nickel (Ni2+), iron (Fe2+) and zinc (Zn2+), assembles to form a biologically active high molecular weight metalloenzyme; a 24-mer with 4-3-2 symmetry. Each 24-mer has 24 active sites, and contains around 1.5 metal ions per monomer, each monomer contributing residues to three separate active sites.
IGPD enzymes are monofunctional in fungi, plants, archaea and some eubacteria while they are encoded as bifunctional enzymes in other eubacteria, such that the enzyme is fused to histidinol-phosphate phosphatase, the penultimate enzyme of the histidine biosynthesis pathway. The histidine biosynthesis pathway is a potential target for development of herbicides, and IGPD is a target for the triazole phosphonate herbicides [
,
,
,
,
,
,
,
,
,
,
,
].Both signature patterns in this entry cover two consecutive, conserved histidine residues.
Imidazoleglycerol-phosphate dehydratase (IGPD;
) catalyzes the dehydration of imidazole glycerol phosphate to imidazole acetol phosphate, the sixth step of histidine biosynthesis in plants and microorganisms where the histidine is synthesized de novo. There is an internal repeat in the protein domain that is related by pseudo-dyad symmetry, perhaps as a result of an ancient gene duplication. The apo-form of IGPD exists as a catalytically inactive trimer which, in the presence of specific divalent metal cations such as manganese (Mn2+), cobalt (Co2+), cadmium (Cd2+), nickel (Ni2+), iron (Fe2+) and zinc (Zn2+), assembles to form a biologically active high molecular weight metalloenzyme; a 24-mer with 4-3-2 symmetry. Each 24-mer has 24 active sites, and contains around 1.5 metal ions per monomer, each monomer contributing residues to three separate active sites.
IGPD enzymes are monofunctional in fungi, plants, archaea and some eubacteria while they are encoded as bifunctional enzymes in other eubacteria, such that the enzyme is fused to histidinol-phosphate phosphatase, the penultimate enzyme of the histidine biosynthesis pathway. The histidine biosynthesis pathway is a potential target for development of herbicides, and IGPD is a target for the triazole phosphonate herbicides [
,
,
,
,
,
,
,
,
,
,
,
].
A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [
,
]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar.They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis.There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble [
]. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp21 is a component of the SSU processome, which is required for pre-18S rRNA processing. It interacts with Utp18 [
].
Rab proteins, a family of small Ras-related GTP-binding proteins, are involved in regulation of
intracellular vesicle trafficking []. Rab GDP dissociation inhibitor (GDI) forms a
soluble complex with Rab proteins, thereby preventing exchange of GDP for GTP. Rab GDI exists in several isoforms, and belongs to the TCD/MRS6 family of GDP dissociation inhibitors.
The crystal structure of the bovine alpha-isoform of Rab GDI has been
determined to a resolution of 1.81A []. The protein is composed of twomain structural units: a large complex multi-sheet domain I, and a smaller
α-helical domain II.The structural organisation of domain I is closely related to FAD-containing
monooxygenases and oxidases []. Conserved regions common to GDI and thechoroideraemia gene product, which delivers Rab to catalytic subunits of
Rab geranylgeranyltransferase II, are clustered on one face of the domain[
]. The two most conserved regions form a compact structure at the apex ofthe molecule; site-directed mutagenesis has shown these regions to play a
critical role in the binding of Rab proteins [].
The lincomycin (LM)-production gene cluster of an over-producing strain of
Streptomyces lincolnensis has been analysed []. The lmb/lmr gene cluster contains 27 open reading frames with putative biosynthetic or
regulatory functions (lmb genes) and three resistance (lmr) genes []. Only a minority of the putative Lmb proteins belong to known proteinfamilies: these include members of the gamma-glutamyl transferases (LmbA);
amino acid acylases (LmbC); aromatic amino acid aminotransferases (LmbF);imidazoleglycerolphosphate dehydratases (LmbK); dTDP-glucose synthases
(LmbO); dTDP-glucose 4,6-dehydratases (LmbM); and (NDP-) ketohexose (or ketocyclitol) aminotransferases (LmbS) [
]. LmbP seems to show some similarity to a family of enzymes that share anN-terminal Gly/Ser-rich putative ATP-binding region: these include galacto-
kinase (), homoserine kinase (
), mevalonate kinase (
) and phosphomevalonate kinase
[]. Sequence v031 from Mycobacterium tuberculosis [] is also a homologue.
Most microorganisms and plants can synthesise thiamin de novo [
]. In this de novo pathway, the thiazole and pyrimidine moieties of thiamin are made separately and coupled together to form thiamin phosphate. For the thiazole moiety, 4-methyl-5-(2-hydroxyethyl)thiazole (THZ), the key salvage step is phosphorylation to give 4-methyl-5-(2-phosphonooxyethyl)thiazole (THZ-P). The enzyme hydoxyethylthiazole kinase () is responsible for this step. Hydoxyethylthiazole kinase is encoded by thiM in Escherichia coli [
] and other bacteria [,
], and by the C-terminal region of bifunctional proteins in some cases, such as Saccharomyces cerevisiae, in which the N-terminal domain corresponds to the bacterial thiamine-phosphate pyrophosphorylase (), ThiE [
,
]. ThiM constitutes a potential target for pro-drug compounds for antibacterial drug development.The Arabidopsis and maize genomes encode homologues of ThiM [
].
This entry represents ankyrin repeat domain-containing protein 13 (ANKRD13). At least 4 subtypes are known to exist, termed A-D. ANKRD13C has been experimentally characterised and acts as a chaperone for biogenesis and folding of the DP receptor for prostaglandin D2 [].
This entry represents the IIIC subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate nucleophile hydrolases. Subfamily III, which includes subfamily IIIA (
) and subfamily IIIB (
) contains sequences which do not contain either of the insert domains between the 1st and 2nd conserved catalytic motifs, subfamily I (
,
,
, and
), or between the 2nd and 3rd, subfamily II (
, and
). Subfamily IIIC contains five relatively distantly related clades: a family of viral proteins (
), a family of eukaryotic proteins called MDP-1 and a family of archaeal proteins most closely related to MDP-1 (), a family of bacteria including the Streptomyces FkbH protein (
), and a small clade including the Pasteurella multocida BcbF and EcbF proteins. The overall lack of species overlap among these clades may indicate a conserved function, but the degree of divergence between the clades and the differences in architecture outside of the domain in some clades warns against such a conclusion.
No member of this subfamily is characterised with respect to function, however the MDP-1 protein [] is a characterised phosphatase. All of the characterised enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases [] are present in subfamily IIIC.
This entry represents two closely related clades of sequences from eukaryotes and archaea, however, some uncharacterised bacterial sequences are also included in this family. The mouse enzyme has been characterised as a phosphatase and has been positively identified as a member of the haloacid dehalogenase (HAD) superfamily by site-directed mutagenesis of the active site residues [
,
]. Its structure is similar to other HAD members but MDP-1 appears to be equally able to dephosphorylate phosphotyrosine and closed-ring phosphosugars [].
Proteins in this family co-localise with COPI vesicle coat proteins [
]. In yeast it is a Golgi membrane protein involved in vesicular trafficking, interacting with Tvp18 and Tvp23 [,
].
Serpins (SERine Proteinase INhibitors) belong to MEROPS inhibitor family I4, clan ID. Most serpin family members are indeed serine protease inhibitors, but several have additional cross-class inhibition functions and inhibit cysteine protease family members such as the caspases and cathepsins [
,
]. Others, such as ovalbumin, are incapable of protease inhibition and serve other functions []. Serpins share a highly conserved core structure that is critical for their functioning as serine protease inhibitors [
]. Inhibitory serpins comprise several α-helix and β-strandstogether with an external reactive centre loop (RCL) containing the active site recognised by the target enzyme. Serpins form covalent complexes with target proteases. Their mechanism of protease inhibition is known as irreversible "trapping", in which a rapid conformational change traps the cognate protease in a covalent complex.
This entry represents a conserved site for the Serpin family of proteins, centred on a well conserved Pro-Phe sequence which is found ten to fifteen residues on the C-terminal side of the reactive bond.
This family of chromatin modification proteins are involved in the regulation of cell cycle progression, apoptosis, and DNA repair. Members are found in yeast, animals and plants. They share significant sequence in their C-terminal regions containing PHD finger domains, which have been implicated in chromatin-mediated transcriptional regulation [
]. The family includes proteins YNG1, YNG2 and Pho23 from Saccharomyces cerevisiae [,
], png1 and png2 from Schizosaccharomyces pombe [], inhibitor of growth proteins ING1-5 from mammals [], and Arabidopsis homologues ING1 (At3g24010) and ING2 (At1g54390) [].
Inhibitor of growth protein, N-terminal histone-binding
Type:
Domain
Description:
Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail.This entry represents the N-terminal histone binding domain found in inhibitor proteins.
This entry contains ribosomal RNA small subunit methyltransferase D as well as the putative rRNA methyltransferase YlbH. They methylate the guanosine in position 966 of 16S rRNA in the assembled 30S particle [
].
Methylmalonate-semialdehyde dehydrogenase (MMSDH,
) catalyses the irreversible NAD+- and CoA-dependent oxidative decarboxylation of methylmalonate semialdehyde to propionyl-CoA. Methylmalonate-semialdehyde dehydrogenase has been characterised in both prokaryotes [
,
] and eukaryotes [], functioning as a mammalian tetramer and a bacterial homodimer. Although similar in monomeric molecular mass and enzymatic activity, the N-terminal sequence in Pseudomonas aeruginosa does not correspond with the N-terminal sequence predicted for rat liver. Sequence homology to a variety of prokaryotic and eukaryotic aldehyde dehydrogenases places MMSDH in the aldehyde dehydrogenase (NAD+) superfamily making MMSDH's CoA requirement unique among known ALDHs. Methylmalonate semialdehyde dehydrogenase is closely related to betaine aldehyde dehydrogenase, 2-hydroxymuconic semialdehyde dehydrogenase, and class 1 and 2 aldehyde dehydrogenase []. In most cases these enzymes are involved in valine metabolism, but Gram-positive bacteria, such as Bacillus, contain a distinct subset. This subset of enzymes is encoded in an iol operon and is apparently involved in myo-inositol catabolism, converting malonic semialdehyde to acetyl CoA ad CO2 [
].
The 4'-phosphopantetheinyl transferase superfamily of proteins transfer the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to the invariant serine of pp-binding. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP []. This superfamily consists of two subtypes: The ACPS type such as ACPS_ECOLI and the Sfp type such as SFP_BACSU. The structure of the Sfp type is known [], which shows the active site accommodates a magnesium ion. The most highly conserved regions of the alignment are involved in binding the magnesium ion.
Coenzyme F420 hydrogenase (
) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C-termini of F420 hydrogenase and dehydrogenase beta subunits [
,
]. The C terminus of Methanobacterium formicicum formate dehydrogenase beta chain (,
) is also represented in this entry [
]. This region is often found in association with the 4Fe-4S binding domain (
), and the N terminus
.
Coenzyme F420 hydrogenase (
) reduces the low-potential two-electron acceptor coenzyme F420. This entry contains the N termini of F420 hydrogenase and dehydrogenase beta subunits [
,
]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (,
) is also represented in this entry [
]. This region is often found in association with the 4Fe-4S binding domain (), and the C terminus
.
Putative membrane protein insertion efficiency factor
Type:
Family
Description:
This family consists of hypothetical membrane protein insertion efficiency factor proteins. They contain three conserved
cysteine residues. They may be involved in insertion of integral membrane proteins into the membrane [].
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.
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 [
].
Nuclear protein AMMECR1, presently a protein of unknown function, is encoded by one of the genes affected by an X-linked deletion that causes the association of Alport syndrome, midface hypoplasia, intellectual disability and elliptocytosis in humans [
]. This entry represents the C-terminal region of AMMECR1 (approximately from residue 122 to 333), which is well conserved. Homologues appear in species ranging from bacteria and archaea to eukaryotes, including Protein PH0010 from Pyrococcus horikoshii [
]. The high level of conservation of the AMMECR1 domain points to a basic cellular function, potentially in either the transcription, replication, repair or translation machinery [,
]. The AMMECR1 domain, which contains a 6-amino-acid motif (LRGCIG) that might be functionally important since it is strikingly conserved throughout evolution []. The AMMECR1 domain consists of two distinct subdomains of different sizes. The large subdomain, which contains both the N- and C-terminal regions, consists of five α-helices and five β-strands. These five β-strands form an antiparallel β-sheet. The small subdomain consists of four α-helices and three β-strands, and these β-strands also form an antiparallel β-sheet. The conserved 'LRGCIG' motif is located at β(2) and its N-terminal loop, and most of the side chains of these residues point toward the interface of the two subdomains. The two subdomains are connected by only two loops, and the interaction between the two subdomains is not strong. Thus, these subdomains may move dynamically when the substrate enters the cleft. The size of the cleft suggests that the substrate is large, e.g., the substrate may be a nucleic acid or protein. However, the inner side of the cleft is not filled with positively charged residues, and therefore it is unlikely that negatively charged nucleic acids such as DNA or RNA interact at this site [].
This entry represents an N-terminal subdomain of the AMMECR1 domain (
). It consists of a 2-layer sandwich structure. Defects in Nuclear protein AMMECR1 (AMMECR1) are involved association of Alport syndrome, midface hypoplasia, intellectual disability and elliptocytosis in humans [
].
Nuclear protein AMMECR1, presently a protein of unknown function, is encoded by one of the genes affected by an X-linked deletion that causes the association of Alport syndrome, midface hypoplasia, intellectual disability and elliptocytosis in humans [
]. Homologues appear in species ranging from bacteria and archaea to eukaryotes, including Protein PH0010 from Pyrococcus horikoshii []. The high level of conservation of the AMMECR1 domain points to a basic cellular function, potentially in either the transcription, replication, repair or translation machinery [,
].
Sialidases (neuraminidases) hydrolyse the non-reducing, terminal sialic acid linkage in various natural substrates, such as glycoproteins, glycolipids, gangliosides, and polysaccharides [
]. In mammals, sialidases occur in the lysosome, the cytosol, and associated with the plasma membrane. Sialidases have also been implicated in the pathogenesis of many diseases. For example, in viruses neuraminidases enable the transport of the virus through mucin, the eruption of the virus from the infected host cell, and the prevention of self-aggregation of virus particles through the destruction of the host cell receptor recognised by the virus []. Eukaryotic, bacterial and viral sialidases share highly conserved regions of β-sheet motifs. Bacterial sialidases often possess domains in addition to the catalytic sialidase domain, for instance the sialidase from Micromonospora viridifaciens contains three domains, of which the catalytic domain described here is the N-terminal domain []. Similarly, leech sialidase is a multidomain protein, where the catalytic domain is the C-terminal domain []. In several paramyxoviruses, sialidase forms part of the multi-functional haemagglutinin-sialidase glycoprotein found on the viral envelope [].
Two different types of thiolase [
,
,
] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase () and 3-ketoacyl-CoA thiolase (
). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.
In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [
].There are two conserved cysteine residues important for thiolase activity. The first located in the N-terminal section of the enzymes is involved in the formation of an acyl-enzyme intermediate; the second, which is found in the signature pattern in this entry, is located at the C-terminal extremity and is the active site base involved in deprotonation in the condensation reaction [].
Thiolases are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and eukaryotes. Two different types of thiolase [
,
,
] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase () and 3-ketoacyl-CoA thiolase (
). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.
In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.There are two conserved cysteine residues important for thiolase activity. The first located in the N-terminal section of the enzymes is involved in the formation of an acyl-enzyme intermediate; the second located at the C-terminal extremity is the active site base involved in deprotonation in the condensation reaction [
].Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [
].The beta-ketothiolases from Haloferax mediterranei BktB and phaA have different substrate specificities and are involved in PHBV biosynthesis [
]. Their catalytic residues have been identified [].
Two different types of thiolase [
,
,
] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase () and 3-ketoacyl-CoA thiolase (
). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.
In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.There are two conserved cysteine residues important for thiolase activity. The first located in the N-terminal section of the enzymes is involved in the formation of an acyl-enzyme intermediate; the second located at the C-terminal extremity is the active site base involved in deprotonation in the condensation reaction [
].Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [
].The signature pattern for this entry is a conserved sequence located towards the C-terminal end.
Small acid-soluble spore protein, alpha/beta-type, conserved site
Type:
Conserved_site
Description:
Small, acid-soluble spore proteins (SASP or ASSP) are proteins bound to the spore DNA of bacteria of the genera Bacillus, Thermoactynomycetes, and Clostridium [
,
]. They are double-stranded DNA-binding proteins that cause DNA to change to an A-like conformation. They protect the DNA backbone from chemical and enzymatic cleavage and are thus involved in dormant spore's high resistance to UV light. SASP are degraded in the first minutes of spore germination and provide amino acids for both new protein synthesis and metabolism.There are two distinct families of SASP: the alpha/beta type and the gamma-type. Alpha/beta SASP are small proteins of about sixty to seventy amino acid residues that are generally coded by a multigene family. The N terminus of alpha/beta SASP contains the site which is cleaved by a SASP-specific protease that acts during germination while the C terminus and is probably involved in DNA-binding.
The N-terminal region of this group of proteins is required for correct folding of the ER UDP-Glc: glucosyltransferase. These proteins selectively reglucosylates unfolded glycoproteins, thus providing quality control for protein transport out of the ER. Unfolded, denatured glycoproteins are substantially better substrates for glucosylation by this enzyme than are the corresponding native proteins. This protein and transient glucosylation may be involved in monitoring and/or assisting the folding and assembly of newly made glycoproteins, in order to identify glycoproteins that need assistance in folding from chaperones
Two types of proteins that hydrolyse inorganic pyrophosphate (PPi), very different in both amino acid sequence and structure, have been characterised to date: soluble and membrane-bound proton-pumping pyrophosphatases (sPPases and H+)-PPases, respectively). sPPases are ubiquitous proteins that hydrolyse PPi to release heat, whereas H+-PPases, so far unidentified in animal and fungal cells, couple the energy of PPi hydrolysis to proton movement across biological membranes [
]. The latter type is represented by this group of proteins. H+-PPases () are also called vacuolar-type inorganic pyrophosphatases (V-PPase) or pyrophosphate-energised vacuolar membrane proton pumps [
]. In plants, vacuoles contain two enzymes for acidifying the interior of the vacuole, the V-ATPase and the V-PPase (V is for vacuolar) []. In Arabidopsis, AVP1 contributes to H+-electrochemical potential difference between the citosol and vacuole lumen and also facilitates auxin transport by modulating apoplastic pH and regulates auxin-mediated developmental processes [].Two distinct biochemical subclasses of H+-PPases have been characterised to date: K+-stimulated and K+-insensitive [
].
Two different types of thiolase [
,
,
] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase () and 3-ketoacyl-CoA thiolase (
). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.
In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [
].There are two conserved cysteine residues important for thiolase activity. The signature pattern for this entry contains the first conserved cysteine located in the N-terminal section of the enzymes, which is involved in the formation of an acyl-enzyme intermediate; the second located at the C-terminal extremity is the active site base involved in deprotonation in the condensation reaction [
].
Small nuclear ribonucleoprotein E (SME1) is involved in pre-mRNA splicing. It is required for pre-mRNA splicing, cap modification and for the stability of snRNA U1, U2, U4 and U5 [
,
].The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons [
,
]. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel β-sheet []. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure [].
Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an α+β structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are [
,
]:Pseudouridine synthase I, TruA.Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.Pseudouridine synthase RluA. TruC, RluC and RluD belong to this family.Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific α+β subdomain.This entry represents a conserved region located in the central part of a group of pseudouridine synthases, predominantly those that belong to the RluA subfamily of pseudouridine synthases, including RluA, RluC, RluD and TruC. These homologous enzymes synthesize pseudouridine from uracil in specific positions [
,
,
]. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis []. RluA shows an elongated, mixed α/β fold, with an with an eight-stranded β-sheet core and additional β-strands, α-helices and loops []. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different [].
Histone proteins have central roles in both chromatin organisation (as
structural units of the nucleosome) and gene regulation (as dynamic componentsthat have a direct impact on DNA transcription and replication). Eukaryotic
DNA wraps around a histone octamer to form a nucleosome, the first order ofcompaction of eukaryotic chromatin. The core histone octamer is composed of a
central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the corehistone contains a common structural motif, called the histone fold, which
facilitates the interactions between the individual core histones.In addition to the core histones, there is a "linker histone"called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures.
Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [,
]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA.The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15
domain is also characterised by high sequence homology among the family oflinker histones. The highly conserved H15 domain is essential for the binding
of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III),with a β-hairpin at the C terminus. There is also a short three-residue
stretch between helices I and II that is in the β-strand conformation.Together with the C-terminal β-hairpin, this strand forms the third strand
of an antiparallel β-sheet [,
,
,
].Histone H5 is a nuclear protein involved in the condensation of nucleosome chains into higher order structures. In this respect, it performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain (residues 22-100) of the linker histone H5, has been solved. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The structure comprises 3 α-helices and 2 short β-strands [
,
].
This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the Saccharomyces cerevisiae Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants [].
Enzymes in this family belong to the ribokinase superfamily. Pyridoxamine kinase
phosphorylates B6 vitamers and functions in a salvage pathway [
,
]. Phosphomethylpyrimidine kinase is part of the thiamine pyrophosphate (TPP) synthesis pathway. TPP is an essential cofactor for many enzymes [
].
This entry represents a bifunctional enzyme, phosphomethylpyrimidine (HMP-P) kinase (
)/Hydroxymethylpyrimidine (HMP) kinase (
), the ThiD/J protein of thiamine biosynthesis. It catalyses two consecutive phosphorylation reactions in the thiamine phosphate biosynthesis pathway, first phosphorylating HMP to HMP-P, and then HMP-P to HMP-PP [
]. The protein is commonly observed within operons containing other thiamine biosynthesis genes. Numerous examples are fusion proteins with other thiamine-biosynthetic domains.
Thiamine phosphate synthase (TPS) catalyses the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate in the thiamine biosynthesis pathway [
].TenI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production belongs to this group [
]. While TenI shows high sequence similarity with thiamin phosphate synthase [], the purified protein has no thiamin phosphate synthase activity. Instead, it is a thiazole tautomerase [].This entry refers to a domain found in thiamine phosphate synthase, thiazole tautomerase and similar proteins.
Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee
King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E.,Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed ofthe first three letters of the genus; a space; the first letter of the
species name; a space and an arabic number. In the event that two speciesnames have identical designations, they are discriminated from one another
by adding one or more letters (as necessary) to each species designation.The allergens in this family include allergens with the following designations: Dol m 5, Pol d 5, Pol e 5, Pol f 5, Sol i 3, Sol r 3, Ves c 5,Ves f 5, Ves g 5, Ves m 5, Ves p 5, Ves s 5, Ves v 5, Ves vi 5 and Vesp m 5.Venom allergen 5 (Ves 5) is a major allergen of vespid wasp venom [
]. Regions of conservation have been identified that areshared both by a family of proteins from human, mouse and rat testis, and
by a class of pathogenesis-related proteins from Nicotiana tabacum (Common tobacco) and Solanum lycopersicum (Tomato) (Lycopersicon esculentum) leaves. Ves 5 also shares similarity with the Solenopsis invicta (Red imported fire ant) 3
allergen [].
The cysteine-rich secretory proteins (Crisp) are predominantly found in the mammalian male reproductive tract as well as in the venom of reptiles. This family includes mammalian testis-specific protein (Tpx-1), also known as cysteine-rich secretory protein 2 (CRISP2) [
]; venom allergen 5 from vespid wasps and venom allergen 3 from fire ants, which are potent allergens that mediate allergic reactions to stings insects of the Hymenoptera family []; scoloptoxins from Scolopendra dehaani (Thai centipede) []; plant pathogenesis proteins of the PR-1 family [], which are synthesised during pathogen infection or other stress-related responses; allurin, a sperm chemoattractant [], serotriflin [], etc.The precise function of some of these proteins is still unclear. Tpx-1 or CRISP2 may regulate some ion channels' activity and thereby regulate calcium fluxes during sperm capacitation [
].This entry also includes allergen Tab y 5.0101 from horsefly salivary glands [
].
2-oxoglutarate dehydrogenase is a key enzyme in the TCA cycle, converting 2-oxoglutarate, coenzyme A and NAD(+) to succinyl-CoA, NADH and carbon dioxide [
]. This activity of this enzyme is tightly regulated and it is a major determinant of the metabolic flux through the TCA cycle. This enzyme is composed of multiple copies of three different subunits: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3) which is often shared with similar enzymes such as pyruvate dehydrogenase []. The E2 component forms a large multimeric core which binds the peripheral E1 and E3 subunits. The substrate is transferred between the active sites of the different subunits by a lipoyl moiety, bound to a lysine residue from the E2 polypeptide.The E1 subunit of 2-oxoglutarate dehydrogenase catalyses the decarboxylation of this compound in a thiamine pyrophosphate-dependent manner, transferring the resultant succinyl group onto the liposyl moiety bound to the E2 subunit. The E1 ortholog from Corynebacterium glutamicum (Brevibacterium flavum) is unusual in having an N-terminal extension that resembles the E2 component of 2-oxoglutarate dehydrogenase enzyme.
This entry represents a domain found in a number of dehydrogenases, all of which use thiamine pyrophosphate as a cofactor and are members of a multienzyme complex:
pyruvate dehydrogenase (
), a component of the multienzyme pyruvate dehydrogenase complex
2-oxoglutarate dehydrogenase (
), a component of the multienzyme 2-oxoglutarate dehydrogenase, which contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3)
2-oxoisovalerate dehydrogenase (
), a component of the multienzyme branched-chain alpha-keto dehydrogenase complex.
This entry represents a structural motif with a beta/alpha TIM barrel found in several proteins families:Endonuclease IV (
), an AP (apurinic/apyrimidinic) endonuclease that primes DNA repair synthesis by cleaving the DNA backbone 5' of AP sites [
].L-rhamnose isomerase (
), a tetramer of four TIM barrels that catalyses the isomerisation between aldoses and ketoses, such as between L-rhamnose and L-rhamnulose [
].Xylose isomerase (
), which catalyses the first reaction in the catabolism of D-xylose by converting D-xylose to D-xylulose [
].Mannonate dehydratase UxuA, which along with mannonate oxidoreductase converts D-fructuronate to 2-keto-3-deoxy-D-gluconate [
].These proteins share similar, but not identical, metal-binding sites. In addition, xylose isomerase and L-rhamnose isomerase each have additional α-helical domains involved in tetramer formation.
Xylose isomerase (
) [
] is an enzyme found in microorganisms which catalyzes the interconversion of D-xylose to D-xylulose. It can also isomerize D-ribose to D-ribulose and D-glucose to D-fructose. The enzyme is a homotetramer, which is stabilised by cobalt, and requires magnesium for its catalytic activity. Each subunit contains 2 domains: the core domain is a parallel α-β barrel; the C-terminal domain is a loop structure consisting of 5 helices and is involved in intermolecular contacts between adjacent subunits []. The active site lies in a deep pocket near the C-terminal ends of the strands of the barrel domain and includes residues from a second subunit. The tetramer is effectively a dimer of "active"dimers, the active sites being composed of residues from both subunits [
].Xylose isomerase also exists in plants [
] where it is homodimeric and is manganese-dependent.
This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.
The beta-CASP domain is found C-terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains [
].
This entry contains proteins belonging to the Yip1 family and represents the Yip1 domain. The Yip1 integral membrane domain contains four transmembrane α-helices. The domain is characterised by the motifs DLYGP and GY. The Yip1 protein is a Golgi protein involved in vesicular transport that interacts with GTPases [
].
This family is found in mammals where it is localised at cell-cell adherens junctions [
], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
This FAD-binding domain can be found in sulfite reductase [NADPH] flavoprotein alpha-component CysJ, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. CysJ is a component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide []. The structure of the nitric oxide synthase FAD-binding domain has been solved [].
This superfamily represents the α-helical subdomain (domain 3) of the FAD-binding domain which can be found in NADPH-cytochrome P450 reductases [
], nitric oxide synthases, NADPH-dependent diflavin oxidoreductases, and pyruvate dehydrogenases.
This entry includes flavodoxins and flavodoxin-like proteins, such as NADPH-dependent diflavin oxidoreductase NDOR1 and nitric oxide synthases. Flavodoxins act in various electron-transport systems as functional
analogues of ferredoxins []. Although flavodoxins are found only in certain bacteria and algae [] the proteins share similarity with a number of protein domains of both prokaryotic and eukaryotic origin [].
Small nuclear ribonucleoproteins (snRNPs) are components of major and minor spliceosomes that play an important role in the splicing of cellular pre-mRNAs. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA. Five small snRNPs (U1, U2, U4 and U5) share the Sm heptamer ring composed of SmB/B', SmD1/2/3, SmE, SmF, and SmG (also known as snRNP-G), while U6 snRNP has a
heptamer ring consist of seven Sm-like (Lsm) proteins: Lsm2, Lsm3, Lsm4, Lsm5, Lsm6, Lsm7 and Lsm8 []. This entry includes the snRNP heptamer ring components SmF (small nuclear ribonucleoprotein F), Lsm6 and LSM36B from
Arabidopsis[
].
Histone H4 is one of the four histones, along with H2A, H2B and H3, which form the eukaryotic nucleosome core. The sequence of histone H4 has remained almost invariant in more then 2 billion years of evolution [
]. The signature pattern for this entry is a pentapeptide found in positions 14 to 18 of all H4 sequences. It contains a lysine residue which is often acetylated [] and a histidine residue which is implicated in DNA-binding [].
Histone H4 is one of the five histones, along with H1/H5, H2A, H2B and H3. Two copies of each of the H2A, H2B, H3, and H4 histones ensemble to form the core of the nucleosome [
]. The nucleosome forms octameric structure that wraps DNA in a left-handed manner. H3 is a highly conserved protein of 135 amino acid residues [,
]. Histones can undergo several different types of post-translational modifications that affect transcription, DNA repair, DNA replication and chromosomal stability. The sequence of histone H4 has remained almost invariant in more then 2 billion years of evolution [,
,
].
The muniscins are a family of endocytic adaptors that is conserved from yeast to humans.This C-terminal domain is structurally similar to mu homology domains, and is the region of the muniscin proteins involved in the interactions with the endocytic adaptor-scaffold proteins Ede1-eps15. This interaction influences muniscin localisation. The muniscins provide a combined adaptor-membrane-tubulation activity that is important for regulating endocytosis [
].
In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolutio has been determined [
]. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed β-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.
In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analogue at 2.5 A resolution has been determined [
]. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The C-terminal domain unexpectedly folds into a compact domain reminiscent of the RNA-recognition motif fold. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase.
Nucleotidytransferases can be divided into two classes based on highly conserved features of the nucleotidyltransferase motif [
]. Class I enzymes include eukaryotic poly(A) polymerase (PAP), archaeal tRNA CCA-adding enzyme and possibly DNA polymerase beta, while class II enzymes include eukaryotic and eubacterial tRNA CCA-adding enzymes. This superfamily represents the C-terminal domain of class I nucleotidyltransferases. The C-terminal domain has an alpha/beta sandwich fold, although the archaeal tRNA CCA-adding enzyme has a large insertion; this fold is reminiscent of the RNA-recognition motif fold. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA. In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. The catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase [
]. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase.The archaeal CCA-adding enzyme builds and repairs the 3 ' end of tRNA. A single active site (nucleotidyltransferase motif) adds both CTP and ATP [
]. This enzyme is the only RNA polymerase that can build or rebuild a specific nucleic acid sequence without using a nucleic acid template.
Cox17p is essential for the assembly of functional cytochrome c oxidase (CCO). Binds and delivers two copper ions to the metallochaperone SCO1 which transports the copper ions to the Cu(A) site on the cytochrome c oxidase subunit II (MT-CO2/COX2) [
,
].
This entry includes 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. It is essential in Escherichia coli. The enzyme is described as "atypical"because it contains a partially-duplicated domain. The family is found in bacteria, where it is widely but not universally distributed, and chloroplasts, where it is essential for chloroplast development [
], salicylic acid-mediated disease resistance to pathogens [] and requires ferrdoxin as a co-factor []. No homology can be detected between this family and other proteins.
This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is largely restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.
Protein translocase complex, SecE/Sec61-gamma subunit
Type:
Family
Description:
Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase
pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them tothe translocase component [
]. From there, the mature proteins are either targeted to the outermembrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial
chromosome.The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral
membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release ofthe mature peptide into the periplasm (SecD and SecF) [
]. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers"in the bacterial cytoplasm.
SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membraneprotein ATPase SecA for secretion [
]. SecE, part of the main SecYEG translocase complex, is ~106 residues in length, and spans the
inner membrane of the Gram-negative bacterial envelope. Together withSecY and SecG, SecE forms a multimeric channel through which preproteins
are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. In eukaryotes, the evolutionary related protein sec61-gamma plays a role in protein translocation through the endoplasmic reticulum; it is part of a trimeric complex that also consist of sec61-alpha and beta [
]. Both secE and sec61-gamma are small proteins of about 60 to 90 amino acids that contain a single transmembrane region at their C-terminal extremity (Escherichia coli secE is an exception, in that it possess an extra N-terminal segment of 60 residues that contains two additional transmembrane domains) [].
This family is the protein translocase SEC61 complex gamma subunit of the archaeal and eukaryotic type. It does not hit bacterial SecE proteins. Sec61 is required for protein translocation in the endoplasmic reticulum.The Sec61 complex (eukaryotes) or SecY complex (prokaryotes) forms a conserved heterotrimeric integral membrane protein complex and forms a protein-conducting channel that allows polypeptides to be transferred across (or integrated into) the endoplasmic reticulum (eukaryotes) or across the cytoplasmic membrane (prokaryotes) [
,
]. This complex is itself a part of a larger translocase heterotrimeric complex composed of alpha, beta and gamma subunits.The channel is a passive conduit for polypeptides. It therefore has to associate with other components that provide a driving force. The partner proteins in bacteria and eukaryotes differ. In bacteria, the translocase complex comprises 7 proteins [
], including a chaperone protein (SecB) an ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD) and SecF. The SecA ATPase interacts dynamically with the SecYEG integral membrane components to drive the transmembrane movement of newly synthesized preproteins []. In yeast (and probably in all eukaryotes), the full translocase comprises another membrane protein subcomplex (the tetrameric Sec62/63p complex), and the lumenal protein BiP, a member of the Hsp70 family of ATPases. BiP promotes translocation by acting as a molecular ratchet, preventing the polypeptide chain from sliding back into the cytosol [
].
The Sec61 complex (eukaryotes) or SecY complex (prokaryotes) forms a conserved heterotrimeric integral membrane protein complex and forms a protein-conducting channel that allows polypeptides to be transferred across (or integrated into) the endoplasmic reticulum (eukaryotes) or across the cytoplasmic membrane (prokaryotes) [
,
]. This complex is composed of alpha, beta and gamma subunits. The alpha-subunits (Sec61-alpha in mammals, Sec61p in Saccharomyces cerevisiae, SecY in bacteria and archaea) and gamma-subunits (Sec61-gamma in mammals, Sss1p in S. cerevisiae, SecE in bacteria and archaea) show significant sequence conservation.The gamma or SecE subunit consists of two α-helices. The N-terminal helix lies on the cytoplasmic surface of the membrane. This helix is amphipathic with the hydrophobic surface pointing towards the membrane, contacting the C-terminal part of the alpha-subunit. This helix is followed by a short β-strand. The second helix is a long, curved transmembrane helix that crosses the membrane at approximately a 35 degrees angle with respect to the plane of the membrane [
].
Survival protein SurE-like phosphatase/nucleotidase
Type:
Domain
Description:
This entry represents a SurE-like structural domain with a 3-layer alpha/bete/alpha topology that bears some topological similarity to the N-terminal domain of the glutaminase/asparaginase family. This domain is found in the stationary phase survival protein SurE, a metal ion-dependent phosphatase found in eubacteria, archaea and eukaryotes. In Escherichia coli,
SurE also has activity as a nucleotidase and exopolyphosphatase, and may be involved in the stress response []. E. coli cells with mutations in the surE gene survive poorly in stationary phase []. The structure of SurE homologues have been determined from Thermotoga maritima [] and the archaea Pyrobaculum aerophilum []. The T. maritima SurE homologue has phosphatase activity that is inhibited by vanadate or tungstate, both of which bind adjacent to the divalent metal ion.
This presumed domain is found at the C terminus of the budding yeast Srp40 and mammalian NOLC1 (also known as Nopp140) proteins. They are nucleolar proteins that contain a central domain consisting of ten repeats of acidic serine clusters alternating with lysine-, alanine- and proline-rich basic stretches [
]. Srp40 may be involved in preribosome assembly or transport []. Human NOLC1 interacts with casein kinase 2 (CK2), RNA polymerase I, p80 coilin , NAP57, and both major classes (box H/ACA and box C/D) of snoRNPs []. It acts as a regulator of RNA polymerase I by connecting RNA polymerase I with enzymes responsible for ribosomal processing and modification [,
].
This family constitutes the major, conserved, portion of PRCC proteins. In humans, this family interacts with MAD2B, the mitotic checkpoint protein [
,
]. In Schizosaccharomyces pombe this protein is part of the Cwf-complex that is known to be involved in pre-mRNA splicing [].
