Protein Domain : Paired DNA-binding domain IPR043182

Type	Domain
Description	The paired domain is a ~126 amino acid DNA-binding domain, which is found in eukaryotic transcription regulatory proteins involved in embryogenesis. The domain was originally described as the 'paired box' in the Drosophila protein paired (prd) [ , ]. The paired DNA-binding domain is generally located in the N-terminal part. An octapeptide [] and/or a homeodomain can occur C-terminal to the paired DNA-binding domain, as well as a Pro-Ser-Thr-rich C-terminal. Paired DNA-binding domain proteins can function as transcription repressors or activators. The paired DNA-binding domain contains three subdomains, which show functional differences in DNA-binding.The crystal structures of prd and Pax proteins show that the DNA-bound paired domain is bipartite, consisting of an N-terminal subdomain (PAI or NTD) and a C-terminal subdomain (RED or CTD), connected by a linker. PAI and RED each form a three-helical fold, with the most C-terminal helices comprising a helix-turn-helix (HTH) motif that binds the DNA major groove. In addition, the PAI subdomain encompasses an N-terminal β-turn andβ-hairpin, also named 'wing', participating in DNA-binding. The linker can bind into the DNA minor groove. Different Pax proteins and their alternatively spliced isoforms use different (sub)domains for DNA-binding to mediate the specificity of sequence recognition [ , ].This entry represents the paired DNA-binding domain. This conserved region spans the DNA-binding HTH located in the N-terminal subdomain.
Short Name	PAIRED_DNA-bd_dom