YEDK_ECOLI
ID YEDK_ECOLI Reviewed; 222 AA.
AC P76318; Q2MB05;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 2.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Abasic site processing protein YedK;
DE EC=3.4.-.- {ECO:0000250|UniProtKB:Q8R1M0};
GN Name=yedK {ECO:0000303|PubMed:29020633}; Synonyms=yedG;
GN OrderedLocusNames=b1931, JW1916;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=JA11;
RX PubMed=8371104; DOI=10.1099/00221287-139-7-1401;
RA Raha M., Kihara M., Kawagishi I., Macnab R.M.;
RT "Organization of the Escherichia coli and Salmonella typhimurium
RT chromosomes between flagellar regions IIIa and IIIb, including a large non-
RT coding region.";
RL J. Gen. Microbiol. 139:1401-1407(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP SEQUENCE REVISION.
RX PubMed=16397293; DOI=10.1093/nar/gkj405;
RA Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R.,
RA Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T.,
RA Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H.,
RA Thomson N.R., Wishart D., Wanner B.L.;
RT "Escherichia coli K-12: a cooperatively developed annotation snapshot
RT -- 2005.";
RL Nucleic Acids Res. 34:1-9(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP IDENTIFICATION.
RX PubMed=23945014; DOI=10.1186/1745-6150-8-20;
RA Aravind L., Anand S., Iyer L.M.;
RT "Novel autoproteolytic and DNA-damage sensing components in the bacterial
RT SOS response and oxidized methylcytosine-induced eukaryotic DNA
RT demethylation systems.";
RL Biol. Direct 8:20-20(2013).
RN [6]
RP ACTIVITY IN VITRO.
RX PubMed=29020633; DOI=10.1016/j.celrep.2017.09.055;
RA Kweon S.M., Zhu B., Chen Y., Aravind L., Xu S.Y., Feldman D.E.;
RT "Erasure of Tet-Oxidized 5-Methylcytosine by a SRAP Nuclease.";
RL Cell Rep. 21:482-494(2017).
RN [7]
RP FUNCTION, AND DNA-BINDING.
RX PubMed=30554877; DOI=10.1016/j.cell.2018.10.055;
RA Mohni K.N., Wessel S.R., Zhao R., Wojciechowski A.C., Luzwick J.W.,
RA Layden H., Eichman B.F., Thompson P.S., Mehta K.P.M., Cortez D.;
RT "HMCES maintains genome integrity by shielding abasic sites in single-
RT strand DNA.";
RL Cell 176:144-153(2019).
RN [8] {ECO:0007744|PDB:6NUA, ECO:0007744|PDB:6NUH}
RP X-RAY CRYSTALLOGRAPHY (1.59 ANGSTROMS) OF 2-222 IN COMPLEX WITH A DNA
RP ABASIC SITE, THIAZOLIDINE LINKAGE TO A DNA ABASIC SITE, FUNCTION, CATALYTIC
RP ACTIVITY, ACTIVE SITE, DOMAIN, AND MUTAGENESIS OF CYS-2; ASN-75; GLU-105
RP AND HIS-160.
RX PubMed=31235915; DOI=10.1038/s41594-019-0255-5;
RA Thompson P.S., Amidon K.M., Mohni K.N., Cortez D., Eichman B.F.;
RT "Protection of abasic sites during DNA replication by a stable thiazolidine
RT protein-DNA cross-link.";
RL Nat. Struct. Mol. Biol. 26:613-618(2019).
RN [9] {ECO:0007744|PDB:6KBS, ECO:0007744|PDB:6KBU, ECO:0007744|PDB:6KBX, ECO:0007744|PDB:6KBZ, ECO:0007744|PDB:6KCQ, ECO:0007744|PDB:6KIJ}
RP X-RAY CRYSTALLOGRAPHY (1.22 ANGSTROMS) OF 2-222 IN COMPLEX WITH A DNA
RP ABASIC SITE, THIAZOLIDINE LINKAGE TO A DNA ABASIC SITE, FUNCTION, CATALYTIC
RP ACTIVITY, ACTIVE SITE, DOMAIN, REACTION MECHANISM, AND MUTAGENESIS OF
RP CYS-2; ARG-4; PRO-40; TRP-67; TRP-68; LYS-70; ASN-75; ARG-77; THR-80;
RP SER-84; ARG-85; GLU-105; TRP-106; LYS-113; THR-149; HIS-160 AND ARG-162.
RX PubMed=31504793; DOI=10.1093/nar/gkz744;
RA Wang N., Bao H., Chen L., Liu Y., Li Y., Wu B., Huang H.;
RT "Molecular basis of abasic site sensing in single-stranded DNA by the SRAP
RT domain of E. coli yedK.";
RL Nucleic Acids Res. 47:10388-10399(2019).
CC -!- FUNCTION: Sensor of abasic sites in single-stranded DNA (ssDNA)
CC required to preserve genome integrity by promoting error-free repair of
CC abasic sites (PubMed:30554877). Recognizes and binds abasic sites in
CC ssDNA at replication forks and chemically modifies the lesion by
CC forming a covalent cross-link with DNA: forms a stable thiazolidine
CC linkage between a ring-opened abasic site and the alpha-amino and
CC sulfhydryl substituents of its N-terminal catalytic cysteine residue
CC (PubMed:30554877, PubMed:31235915, PubMed:31504793). May act as a
CC protease: mediates autocatalytic processing of its N-terminal
CC methionine in order to expose the catalytic cysteine (By similarity).
CC {ECO:0000250|UniProtKB:Q8R1M0, ECO:0000269|PubMed:30554877,
CC ECO:0000269|PubMed:31235915, ECO:0000269|PubMed:31504793}.
CC -!- DOMAIN: Glu-105 is involved in sensing abasic sites in single-stranded
CC DNA (ssDNA) (PubMed:31504793). His-160 stabilizes the abasic sites by
CC forming a hydrogen bond with the O4' hydroxyl group (PubMed:31235915).
CC {ECO:0000269|PubMed:31235915, ECO:0000269|PubMed:31504793}.
CC -!- MISCELLANEOUS: The thiol group of the catalytic Cys-2 is deprotonated
CC by its alpha-amino group to form a thiolate anion that is poised for
CC catalysis (PubMed:31504793). The abasic site sugar moiety is in
CC equilibrium between its cyclic furanose and open-chain aldehyde forms
CC (PubMed:31504793). The Cys-2 thiolate anion attacks the abasic site C1'
CC position to form a covalent bond (PubMed:31504793). The Cys-2 alpha-
CC amino group proton then transfers to the oxygen which is stabilized by
CC the Asn-75 side chain (PubMed:31504793). The O4' rotates to a new
CC position and interacts with the His-160 side chain (PubMed:31504793).
CC The Cys-2 alpha-amino group then attacks the C1' position and transfers
CC a proton to the hydroxyl group to release a water molecule, meanwhile
CC forming a covalent bond with the C1' atom (PubMed:31504793). Thus, a
CC thiazolidine linkage is formed between the abasic site C1' atom and the
CC Cys-2 amino and thiol groups (PubMed:31504793). The Glu-105 side chain
CC carboxyl stabilizes the thiazolidine linkage via a strong hydrogen bond
CC with its amine group (PubMed:31504793). {ECO:0000269|PubMed:31504793}.
CC -!- SIMILARITY: Belongs to the SOS response-associated peptidase family.
CC {ECO:0000305}.
CC -!- CAUTION: Was reported to act as an endonuclease that specifically
CC cleaves 5-hydroxymethylcytosine (5hmC)-containing DNA in vitro
CC (PubMed:29020633). Additional experiments are however required to
CC confirm this activity as this protein is present in many organisms that
CC do not utilize methylcytosine for epigenetic control.
CC {ECO:0000269|PubMed:29020633, ECO:0000305|PubMed:30554877}.
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DR EMBL; L13279; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U00096; AAT48139.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76551.1; -; Genomic_DNA.
DR PIR; H64956; H64956.
DR RefSeq; WP_000334583.1; NZ_LN832404.1.
DR RefSeq; YP_025310.1; NC_000913.3.
DR PDB; 2ICU; X-ray; 1.60 A; A/B=1-222.
DR PDB; 6KBS; X-ray; 1.60 A; B=2-222.
DR PDB; 6KBU; X-ray; 2.10 A; A/B=2-222.
DR PDB; 6KBX; X-ray; 1.22 A; B=2-222.
DR PDB; 6KBZ; X-ray; 1.65 A; B/D/F/H=2-222.
DR PDB; 6KCQ; X-ray; 1.70 A; B=1-222.
DR PDB; 6KIJ; X-ray; 1.58 A; B=2-222.
DR PDB; 6NUA; X-ray; 1.64 A; A/B=2-222.
DR PDB; 6NUH; X-ray; 1.59 A; A=2-222.
DR PDBsum; 2ICU; -.
DR PDBsum; 6KBS; -.
DR PDBsum; 6KBU; -.
DR PDBsum; 6KBX; -.
DR PDBsum; 6KBZ; -.
DR PDBsum; 6KCQ; -.
DR PDBsum; 6KIJ; -.
DR PDBsum; 6NUA; -.
DR PDBsum; 6NUH; -.
DR AlphaFoldDB; P76318; -.
DR SMR; P76318; -.
DR BioGRID; 4261039; 9.
DR IntAct; P76318; 14.
DR STRING; 511145.b1931; -.
DR jPOST; P76318; -.
DR PaxDb; P76318; -.
DR PRIDE; P76318; -.
DR EnsemblBacteria; AAT48139; AAT48139; b1931.
DR EnsemblBacteria; BAE76551; BAE76551; BAE76551.
DR GeneID; 946435; -.
DR KEGG; ecj:JW1916; -.
DR KEGG; eco:b1931; -.
DR PATRIC; fig|511145.12.peg.2013; -.
DR EchoBASE; EB3063; -.
DR eggNOG; COG2135; Bacteria.
DR HOGENOM; CLU_035990_6_1_6; -.
DR InParanoid; P76318; -.
DR OMA; FPARYNI; -.
DR PhylomeDB; P76318; -.
DR BioCyc; EcoCyc:EG11662-MON; -.
DR BioCyc; MetaCyc:EG11662-MON; -.
DR EvolutionaryTrace; P76318; -.
DR PRO; PR:P76318; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008233; F:peptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0003697; F:single-stranded DNA binding; IDA:UniProtKB.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IDA:UniProtKB.
DR GO; GO:0018142; P:protein-DNA covalent cross-linking; IDA:UniProtKB.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0009432; P:SOS response; IEA:UniProtKB-KW.
DR Gene3D; 3.90.1680.10; -; 1.
DR InterPro; IPR003738; SRAP.
DR InterPro; IPR036590; SRAP-like.
DR PANTHER; PTHR13604; PTHR13604; 1.
DR Pfam; PF02586; SRAP; 1.
DR SUPFAM; SSF143081; SSF143081; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Covalent protein-DNA linkage; DNA damage; DNA-binding;
KW Hydrolase; Protease; Reference proteome; SOS response.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:Q8R1M0"
FT CHAIN 2..222
FT /note="Abasic site processing protein YedK"
FT /id="PRO_0000169094"
FT ACT_SITE 2
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:31235915,
FT ECO:0000269|PubMed:31504793"
FT SITE 105
FT /note="Required for sensing abasic sites"
FT /evidence="ECO:0000269|PubMed:31504793"
FT SITE 160
FT /note="Required to stabilize abasic sites"
FT /evidence="ECO:0000269|PubMed:31235915"
FT MOD_RES 2
FT /note="Thiazolidine linkage to a ring-opened DNA abasic
FT site"
FT /evidence="ECO:0000269|PubMed:31235915,
FT ECO:0000269|PubMed:31504793"
FT MUTAGEN 2
FT /note="C->A: Abolished formation of the DNA-protein cross-
FT link. Reduced binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31235915,
FT ECO:0000269|PubMed:31504793"
FT MUTAGEN 2
FT /note="C->S: Abolished formation of the DNA-protein cross-
FT link, possibly via the formation of an oxazolidine ring
FT with DNA that is not as stable as a thiazolidine."
FT /evidence="ECO:0000269|PubMed:31235915"
FT MUTAGEN 4
FT /note="R->A: Reduced binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 40
FT /note="P->G: Reduced binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 67
FT /note="W->A: Abolished binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 68
FT /note="W->A: Abolished binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 70
FT /note="K->A: Slightly reduced binding to single-stranded
FT DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 75
FT /note="N->A: Reduced formation of the DNA-protein cross-
FT link. Reduced binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31235915,
FT ECO:0000269|PubMed:31504793"
FT MUTAGEN 77
FT /note="R->A: Abolished binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 80
FT /note="T->A: Reduced binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 84
FT /note="S->A: Reduced binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 85
FT /note="R->A: Strongly reduced binding to single-stranded
FT DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 105
FT /note="E->A: Reduced formation of the DNA-protein cross-
FT link. Increased binding to single-stranded DNA and further
FT increased affinity for single-stranded DNA containing an
FT abasic site."
FT /evidence="ECO:0000269|PubMed:31235915,
FT ECO:0000269|PubMed:31504793"
FT MUTAGEN 106
FT /note="W->A: Reduced binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 113
FT /note="K->A: Does not affect binding to single-stranded
FT DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 149
FT /note="T->A: Reduced formation of the DNA-protein cross-
FT link. Abolished binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT MUTAGEN 160
FT /note="H->A: Reduced formation of the DNA-protein cross-
FT link. Slightly increased binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31235915,
FT ECO:0000269|PubMed:31504793"
FT MUTAGEN 162
FT /note="R->A: Abolished binding to single-stranded DNA."
FT /evidence="ECO:0000269|PubMed:31504793"
FT STRAND 4..7
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 11..15
FT /evidence="ECO:0007829|PDB:6KBX"
FT TURN 16..18
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 21..23
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 42..50
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 53..61
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:6KBX"
FT TURN 78..80
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 81..83
FT /evidence="ECO:0007829|PDB:6KBX"
FT TURN 85..87
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 88..93
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 95..109
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 112..120
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 145..151
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 154..158
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 161..164
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 169..176
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 182..192
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:6KBX"
FT STRAND 199..203
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 206..209
FT /evidence="ECO:0007829|PDB:6KBX"
FT HELIX 216..219
FT /evidence="ECO:0007829|PDB:6KBX"
SQ SEQUENCE 222 AA; 24979 MW; E203A1EA67119F1C CRC64;
MCGRFAQSQT REDYLALLAE DIERDIPYDP EPIGRYNVAP GTKVLLLSER DEHLHLDPVF
WGYAPGWWDK PPLINARVET AATSRMFKPL WQHGRAICFA DGWFEWKKEG DKKQPFFIYR
ADGQPIFMAA IGSTPFERGD EAEGFLIVTA AADQGLVDIH DRRPLVLSPE AAREWMRQEI
SGKEASEIAA SGCVPANQFS WHPVSRAVGN VKNQGAELIQ PV
