UniProtKB - P76318 (YEDK_ECOLI)
Protein
Abasic site processing protein YedK
Gene
yedK
Organism
Escherichia coli (strain K12)
Status
Functioni
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). May act as a protease: mediates autocatalytic processing of its N-terminal methionine in order to expose the catalytic cysteine (By similarity).By similarity3 Publications
Miscellaneous
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).1 Publication
Caution
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.1 Publication1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 2 | Nucleophile2 Publications | 1 | |
Sitei | 105 | Required for sensing abasic sites1 Publication | 1 | |
Sitei | 160 | Required to stabilize abasic sites1 Publication | 1 |
GO - Molecular functioni
- peptidase activity Source: UniProtKB-KW
- single-stranded DNA binding Source: UniProtKB
GO - Biological processi
- cellular response to DNA damage stimulus Source: UniProtKB
- protein-DNA covalent cross-linking Source: UniProtKB
- SOS response Source: UniProtKB-KW
Keywordsi
Molecular function | DNA-binding, Hydrolase, Protease |
Biological process | DNA damage, SOS response |
Enzyme and pathway databases
BioCyci | EcoCyc:EG11662-MONOMER MetaCyc:EG11662-MONOMER |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:yedK1 Publication Synonyms:yedG Ordered Locus Names:b1931, JW1916 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 2 | C → A: Abolished formation of the DNA-protein cross-link. Reduced binding to single-stranded DNA. 2 Publications | 1 | |
Mutagenesisi | 2 | C → S: Abolished formation of the DNA-protein cross-link, possibly via the formation of an oxazolidine ring with DNA that is not as stable as a thiazolidine. 1 Publication | 1 | |
Mutagenesisi | 4 | R → A: Reduced binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 40 | P → G: Reduced binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 67 | W → A: Abolished binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 68 | W → A: Abolished binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 70 | K → A: Slightly reduced binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 75 | N → A: Reduced formation of the DNA-protein cross-link. Reduced binding to single-stranded DNA. 2 Publications | 1 | |
Mutagenesisi | 77 | R → A: Abolished binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 80 | T → A: Reduced binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 84 | S → A: Reduced binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 85 | R → A: Strongly reduced binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 105 | E → A: Reduced formation of the DNA-protein cross-link. Increased binding to single-stranded DNA and further increased affinity for single-stranded DNA containing an abasic site. 2 Publications | 1 | |
Mutagenesisi | 106 | W → A: Reduced binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 113 | K → A: Does not affect binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 149 | T → A: Reduced formation of the DNA-protein cross-link. Abolished binding to single-stranded DNA. 1 Publication | 1 | |
Mutagenesisi | 160 | H → A: Reduced formation of the DNA-protein cross-link. Slightly increased binding to single-stranded DNA. 2 Publications | 1 | |
Mutagenesisi | 162 | R → A: Abolished binding to single-stranded DNA. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | RemovedBy similarity | |||
ChainiPRO_0000169094 | 2 – 222 | Abasic site processing protein YedKAdd BLAST | 221 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 2 | Thiazolidine linkage to a ring-opened DNA abasic site2 Publications | 1 |
Keywords - PTMi
Covalent protein-DNA linkageProteomic databases
jPOSTi | P76318 |
PaxDbi | P76318 |
PRIDEi | P76318 |
Interactioni
Protein-protein interaction databases
BioGRIDi | 4261039, 9 interactors |
IntActi | P76318, 14 interactors |
STRINGi | 511145.b1931 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P76318 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P76318 |
Family & Domainsi
Domaini
Glu-105 is 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).2 Publications
Sequence similaritiesi
Belongs to the SOS response-associated peptidase family.Curated
Phylogenomic databases
eggNOGi | COG2135, Bacteria |
HOGENOMi | CLU_035990_6_1_6 |
InParanoidi | P76318 |
PhylomeDBi | P76318 |
Family and domain databases
Gene3Di | 3.90.1680.10, 1 hit |
InterProi | View protein in InterPro IPR003738, SRAP IPR036590, SRAP-like |
PANTHERi | PTHR13604, PTHR13604, 1 hit |
Pfami | View protein in Pfam PF02586, SRAP, 1 hit |
SUPFAMi | SSF143081, SSF143081, 1 hit |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
P76318-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MCGRFAQSQT REDYLALLAE DIERDIPYDP EPIGRYNVAP GTKVLLLSER
60 70 80 90 100
DEHLHLDPVF WGYAPGWWDK PPLINARVET AATSRMFKPL WQHGRAICFA
110 120 130 140 150
DGWFEWKKEG DKKQPFFIYR ADGQPIFMAA IGSTPFERGD EAEGFLIVTA
160 170 180 190 200
AADQGLVDIH DRRPLVLSPE AAREWMRQEI SGKEASEIAA SGCVPANQFS
210 220
WHPVSRAVGN VKNQGAELIQ PV
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L13279 Genomic DNA No translation available. U00096 Genomic DNA Translation: AAT48139.1 AP009048 Genomic DNA Translation: BAE76551.1 |
PIRi | H64956 |
RefSeqi | WP_000334583.1, NZ_LN832404.1 YP_025310.1, NC_000913.3 |
Genome annotation databases
EnsemblBacteriai | AAT48139; AAT48139; b1931 BAE76551; BAE76551; BAE76551 |
GeneIDi | 946435 |
KEGGi | ecj:JW1916 eco:b1931 |
PATRICi | fig|511145.12.peg.2013 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L13279 Genomic DNA No translation available. U00096 Genomic DNA Translation: AAT48139.1 AP009048 Genomic DNA Translation: BAE76551.1 |
PIRi | H64956 |
RefSeqi | WP_000334583.1, NZ_LN832404.1 YP_025310.1, NC_000913.3 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2ICU | X-ray | 1.60 | A/B | 1-222 | [»] | |
6KBS | X-ray | 1.60 | B | 2-222 | [»] | |
6KBU | X-ray | 2.10 | A/B | 2-222 | [»] | |
6KBX | X-ray | 1.22 | B | 2-222 | [»] | |
6KBZ | X-ray | 1.65 | B/D/F/H | 2-222 | [»] | |
6KCQ | X-ray | 1.70 | B | 1-222 | [»] | |
6KIJ | X-ray | 1.58 | B | 2-222 | [»] | |
6NUA | X-ray | 1.64 | A/B | 2-222 | [»] | |
6NUH | X-ray | 1.59 | A | 2-222 | [»] | |
SMRi | P76318 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4261039, 9 interactors |
IntActi | P76318, 14 interactors |
STRINGi | 511145.b1931 |
Proteomic databases
jPOSTi | P76318 |
PaxDbi | P76318 |
PRIDEi | P76318 |
Genome annotation databases
EnsemblBacteriai | AAT48139; AAT48139; b1931 BAE76551; BAE76551; BAE76551 |
GeneIDi | 946435 |
KEGGi | ecj:JW1916 eco:b1931 |
PATRICi | fig|511145.12.peg.2013 |
Organism-specific databases
EchoBASEi | EB3063 |
Phylogenomic databases
eggNOGi | COG2135, Bacteria |
HOGENOMi | CLU_035990_6_1_6 |
InParanoidi | P76318 |
PhylomeDBi | P76318 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG11662-MONOMER MetaCyc:EG11662-MONOMER |
Miscellaneous databases
EvolutionaryTracei | P76318 |
PROi | PR:P76318 |
Family and domain databases
Gene3Di | 3.90.1680.10, 1 hit |
InterProi | View protein in InterPro IPR003738, SRAP IPR036590, SRAP-like |
PANTHERi | PTHR13604, PTHR13604, 1 hit |
Pfami | View protein in Pfam PF02586, SRAP, 1 hit |
SUPFAMi | SSF143081, SSF143081, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | YEDK_ECOLI | |
Accessioni | P76318Primary (citable) accession number: P76318 Secondary accession number(s): Q2MB05 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | November 1, 1997 |
Last sequence update: | October 11, 2004 | |
Last modified: | April 7, 2021 | |
This is version 124 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families