This SH3 domain is found central in exodeoxyribonuclease I/Exonuclease I ([interpro:IPR013520]), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in Escherichia coli is associated with DNA deoxyribophosphodiesterase (dRPase) [[cite:PUB00020975]].
","llm":false,"checked":false,"updated":false},{"text":"In bacteria, exonuclease I (ExoI) is a monomeric processive 3'-5' exonuclease that degrades single-stranded DNA. The enzyme has been implicated as primarily being involved in repairing frameshift mutations. ExoI consists of three domains: an N-terminal nuclease domain ([interpro:IPR013520]) with homology to the proofreading domain of E. coli DNA polymerase I and other DnaQ superfamily enzymes, a central domain ([interpro:IPR013620]) with a portion that resembles an SH3 domain fold and a C-terminal α-helical domain. While a typical SH3-like domain consists of five or six antiparallel β-strands that form a compact β-barrel, the β-barrel of the SH3-like domain in ExoI is surrounded by α-helices, resulting in a substantially elaborated fold [[cite:PUB00021628], [cite:PUB00049176], [cite:PUB00067024]].
","llm":false,"checked":false,"updated":false}],"wikipedia":null,"literature":{"PUB00020975":{"PMID":1329027,"ISBN":null,"volume":"20","issue":"18","year":1992,"title":"DNA deoxyribophosphodiesterase of Escherichia coli is associated with exonuclease I.","URL":null,"raw_pages":"4699-703","medline_journal":"Nucleic Acids Res","ISO_journal":"Nucleic Acids Res.","authors":["Sandigursky M","Franklin WA."],"DOI_URL":"http://dx.doi.org/10.1093/nar/20.18.4699"},"PUB00021628":{"PMID":11101894,"ISBN":null,"volume":"7","issue":"12","year":2000,"title":"Structure of Escherichia coli exonuclease I suggests how processivity is achieved.","URL":null,"raw_pages":"1125-8","medline_journal":"Nat Struct Biol","ISO_journal":"Nat. Struct. Biol.","authors":["Breyer WA","Matthews BW."],"DOI_URL":"http://dx.doi.org/10.1038/81978"},"PUB00049176":{"PMID":18219121,"ISBN":null,"volume":"64","issue":"Pt 2","year":2008,"title":"Structure of Escherichia coli exonuclease I in complex with thymidine 5'-monophosphate.","URL":null,"raw_pages":"206-10","medline_journal":"Acta Crystallogr D Biol Crystallogr","ISO_journal":"Acta Crystallogr. D Biol. Crystallogr.","authors":["Busam RD."],"DOI_URL":"http://dx.doi.org/10.1107/S090744490706012X"},"PUB00067024":{"PMID":23609540,"ISBN":null,"volume":null,"issue":null,"year":2013,"title":"Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion.","URL":null,"raw_pages":null,"medline_journal":"Nucleic Acids Res","ISO_journal":"Nucleic Acids Res.","authors":["Korada SK","Johns TD","Smith CE","Jones ND","McCabe KA","Bell CE."],"DOI_URL":null}},"set_info":null,"overlaps_with":[{"accession":"IPR012337","name":"Ribonuclease H-like superfamily","type":"homologous_superfamily"},{"accession":"IPR038649","name":"Exonuclease I, SH3-like domain superfamily","type":"homologous_superfamily"}],"counters":{"subfamilies":0,"domain_architectures":10,"interactions":0,"matches":5749,"pathways":0,"proteins":5748,"proteomes":3078,"sets":0,"structural_models":{"alphafold":4470,"bfvd":0},"structures":13,"taxa":5140},"entry_annotations":{"alignment:seed":82,"alignment:full":1262},"cross_references":{"ec":{"displayName":"ENZYME","description":"ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.","rank":19,"accessions":[{"accession":"3.1.11.1","url":"https://enzyme.expasy.org/EC/3.1.11.1"}]}},"is_llm":false,"is_reviewed_llm":false,"is_updated_llm":false,"representative_structure":null}}