{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"P76318","secondaryAccessions":["Q2MB05"],"uniProtkbId":"YEDK_ECOLI","entryAudit":{"firstPublicDate":"1997-11-01","lastAnnotationUpdateDate":"2026-09-02","lastSequenceUpdateDate":"2004-10-11","entryVersion":145,"sequenceVersion":2},"annotationScore":5.0,"organism":{"scientificName":"Escherichia coli (strain K12)","taxonId":83333,"lineage":["Bacteria","Pseudomonadati","Pseudomonadota","Gammaproteobacteria","Enterobacterales","Enterobacteriaceae","Escherichia"]},"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"Abasic site processing protein YedK"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31504793"}],"value":"4.-.-.-"}]},"alternativeNames":[{"fullName":{"value":"Peptidase YedK"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q8R1M0"}],"value":"3.4.-.-"}]}]},"genes":[{"geneName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"29020633"}],"value":"yedK"},"synonyms":[{"value":"yedG"}],"orderedLocusNames":[{"value":"b1931"},{"value":"JW1916"}]}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q8R1M0"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"30554877"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31235915"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31504793"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"35934051"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"37519246"}],"value":"Sensor of abasic sites in single-stranded DNA (ssDNA) required to preserve genome integrity by promoting error-free repair of abasic sites (PubMed:30554877). Recognizes and binds abasic sites in ssDNA at replication forks and chemically modifies the lesion by forming a covalent cross-link with DNA: forms a stable thiazolidine linkage between a ring-opened abasic site and the alpha-amino and sulfhydryl substituents of its N-terminal catalytic cysteine residue (PubMed:30554877, PubMed:31235915, PubMed:31504793). The DNA-protein cross-link is then reversed: able to catalyze the reversal of the thiazolidine cross-link and cycle between a cross-link and a non-cross-linked state depending on DNA context: mediates self-reversal of the thiazolidine cross-link in double stranded DNA (PubMed:35934051, PubMed:37519246). May act as a protease: mediates autocatalytic processing of its N-terminal methionine in order to expose the catalytic cysteine (By similarity)"}],"commentType":"FUNCTION"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96FZ2"}],"value":"Formation and reversal of DNA-protein cross-link depends on DNA context. Catalyzes formation of the thiazolidine linkage in presence of abasic sites in single-stranded DNA. Mediates the reversal of the thiazolidine cross-link in presence of double stranded DNA"}],"commentType":"ACTIVITY REGULATION"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q96FZ2"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31235915"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31504793"}],"value":"The N-terminal catalytic Cys-2 residue forms a thiazolidine linkage to a ring-opened DNA abasic site (PubMed:31235915, PubMed:31504793). Glu-105 catalyzes reversal of the thiazolidine linkage; self-reversal is favoured by duplex DNA formation (By similarity). Glu-105 is also involved in sensing abasic sites in single-stranded DNA (ssDNA) (PubMed:31504793). His-160 stabilizes the abasic sites by forming a hydrogen bond with the O4' hydroxyl group (PubMed:31235915)"}],"commentType":"DOMAIN"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31504793"}],"value":"The thiol group of the catalytic Cys-2 is deprotonated by its alpha-amino group to form a thiolate anion that is poised for catalysis (PubMed:31504793). The abasic site sugar moiety is in equilibrium between its cyclic furanose and open-chain aldehyde forms (PubMed:31504793). The Cys-2 thiolate anion attacks the abasic site C1' position to form a covalent bond (PubMed:31504793). The Cys-2 alpha-amino group proton then transfers to the oxygen which is stabilized by the Asn-75 side chain (PubMed:31504793). The O4' rotates to a new position and interacts with the His-160 side chain (PubMed:31504793). The Cys-2 alpha-amino group then attacks the C1' position and transfers a proton to the hydroxyl group to release a water molecule, meanwhile forming a covalent bond with the C1' atom (PubMed:31504793). Thus, a thiazolidine linkage is formed between the abasic site C1' atom and the Cys-2 amino and thiol groups (PubMed:31504793). The Glu-105 side chain carboxyl stabilizes the thiazolidine linkage via a strong hydrogen bond with its amine group (PubMed:31504793)"}],"commentType":"MISCELLANEOUS"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"Belongs to the SOS response-associated peptidase family"}],"commentType":"SIMILARITY"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"29020633"},{"evidenceCode":"ECO:0000305","source":"PubMed","id":"30554877"}],"value":"Was reported to act as an endonuclease that specifically cleaves 5-hydroxymethylcytosine (5hmC)-containing DNA in vitro (PubMed:29020633). Additional experiments are however required to confirm this activity as this protein is present in many organisms that do not utilize methylcytosine for epigenetic control"}],"commentType":"CAUTION"}],"features":[{"type":"Initiator methionine","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":1,"modifier":"EXACT"}},"description":"Removed","evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"Q8R1M0"}]},{"type":"Chain","location":{"start":{"value":2,"modifier":"EXACT"},"end":{"value":222,"modifier":"EXACT"}},"description":"Abasic site processing protein YedK","featureId":"PRO_0000169094"},{"type":"Active site","location":{"start":{"value":2,"modifier":"EXACT"},"end":{"value":2,"modifier":"EXACT"}},"description":"Nucleophile","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31235915"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31504793"}]},{"type":"Active site","location":{"start":{"value":105,"modifier":"EXACT"},"end":{"value":105,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"35934051"},{"evidenceCode":"ECO:0000305","source":"PubMed","id":"37519246"}]},{"type":"Site","location":{"start":{"value":105,"modifier":"EXACT"},"end":{"value":105,"modifier":"EXACT"}},"description":"Required for sensing abasic sites","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31504793"}]},{"type":"Site","location":{"start":{"value":160,"modifier":"EXACT"},"end":{"value":160,"modifier":"EXACT"}},"description":"Required to stabilize abasic sites","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31235915"}]},{"type":"Modified residue","location":{"start":{"value":2,"modifier":"EXACT"},"end":{"value":2,"modifier":"EXACT"}},"description":"Thiazolidine linkage to a ring-opened DNA abasic site","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31235915"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"31504793"}]},{"type":"Mutagenesis","location":{"start":{"value":2,"modifier":"EXACT"},"end":{"value":2,"modifier":"EXACT"}},"description":"Abolished formation of the DNA-protein cross-link. 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