VSR_ECOLI
ID VSR_ECOLI Reviewed; 156 AA.
AC P09184;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=DNA mismatch endonuclease Vsr;
DE EC=3.1.-.-;
DE AltName: Full=Type II nicking enzyme {ECO:0000303|PubMed:12654995};
DE AltName: Full=V.EcoKDcm {ECO:0000303|PubMed:12654995};
DE AltName: Full=Very short patch repair protein;
DE AltName: Full=Vsr mismatch endonuclease {ECO:0000303|PubMed:1944537};
GN Name=vsr {ECO:0000303|PubMed:2198248}; OrderedLocusNames=b1960, JW1943;
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=K12;
RX PubMed=2527357; DOI=10.1093/nar/17.14.5844;
RA Hanck T., Gerwin N., Fritz H.-J.;
RT "Nucleotide sequence of the dcm locus of Escherichia coli K12.";
RL Nucleic Acids Res. 17:5844-5844(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2198248; DOI=10.1128/jb.172.8.4214-4221.1990;
RA Sohail A., Lieb M., Dar M., Bhagwat A.S.;
RT "A gene required for very short patch repair in Escherichia coli is
RT adjacent to the DNA cytosine methylase gene.";
RL J. Bacteriol. 172:4214-4221(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA Horiuchi T.;
RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 40.1-50.0 min region on the linkage map.";
RL DNA Res. 3:379-392(1996).
RN [4]
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 [5]
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 [6]
RP FUNCTION.
RX PubMed=1944537; DOI=10.1038/353776a0;
RA Hennecke F., Kolmar H., Bruendi K., Fritz H.-J.;
RT "The vsr gene product of E. coli K-12 is a strand- and sequence-specific
RT DNA mismatch endonuclease.";
RL Nature 353:776-778(1991).
RN [7]
RP FUNCTION.
RX PubMed=10871403; DOI=10.1093/nar/28.13.2535;
RA Fox K.R., Allinson S.L., Sahagun-Krause H., Brown T.;
RT "Recognition of GT mismatches by Vsr mismatch endonuclease.";
RL Nucleic Acids Res. 28:2535-2540(2000).
RN [8]
RP NOMENCLATURE.
RX PubMed=12654995; DOI=10.1093/nar/gkg274;
RA Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A.,
RA Bitinaite J., Blumenthal R.M., Degtyarev S.K., Dryden D.T., Dybvig K.,
RA Firman K., Gromova E.S., Gumport R.I., Halford S.E., Hattman S.,
RA Heitman J., Hornby D.P., Janulaitis A., Jeltsch A., Josephsen J., Kiss A.,
RA Klaenhammer T.R., Kobayashi I., Kong H., Krueger D.H., Lacks S.,
RA Marinus M.G., Miyahara M., Morgan R.D., Murray N.E., Nagaraja V.,
RA Piekarowicz A., Pingoud A., Raleigh E., Rao D.N., Reich N., Repin V.E.,
RA Selker E.U., Shaw P.C., Stein D.C., Stoddard B.L., Szybalski W.,
RA Trautner T.A., Van Etten J.L., Vitor J.M., Wilson G.G., Xu S.Y.;
RT "A nomenclature for restriction enzymes, DNA methyltransferases, homing
RT endonucleases and their genes.";
RL Nucleic Acids Res. 31:1805-1812(2003).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
RX PubMed=10612397; DOI=10.1016/s0092-8674(00)81550-0;
RA Tsutakawa S.E., Jingami H., Morikawa K.;
RT "Recognition of a TG mismatch: the crystal structure of very short patch
RT repair endonuclease in complex with a DNA duplex.";
RL Cell 99:615-623(1999).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 22-157.
RX PubMed=10360178; DOI=10.1016/s1097-2765(00)80355-x;
RA Tsutakawa S.E., Muto T., Kawate T., Jingami H., Kunishima N., Ariyoshi M.,
RA Kohda D., Nakagawa M., Morikawa K.;
RT "Crystallographic and functional studies of very short patch repair
RT endonuclease.";
RL Mol. Cell 3:621-628(1999).
CC -!- FUNCTION: Deamination of 5-methylcytosine in DNA results in T/G
CC mismatches. If unrepaired, these mismatches can lead to C-to-T
CC transition mutations. The very short patch (VSP) repair process in
CC E.coli counteracts the mutagenic process by repairing the mismatches in
CC favor of the G-containing strand. This enzyme is an endonuclease that
CC nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next
CC to the thymidine residue that is mismatched to 2'-deoxyguanosine. The
CC incision is mismatch-dependent and strand-specific.
CC {ECO:0000269|PubMed:10871403, ECO:0000269|PubMed:1944537}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 2 magnesium ions per subunit.;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Note=Binds 1 zinc ion per subunit.;
CC -!- INTERACTION:
CC P09184; P23367: mutL; NbExp=3; IntAct=EBI-765033, EBI-554913;
CC -!- SIMILARITY: Belongs to the Vsr family. {ECO:0000305}.
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DR EMBL; X13330; CAA31707.1; -; Genomic_DNA.
DR EMBL; M32307; AAA03724.1; -; Unassigned_DNA.
DR EMBL; U00096; AAC75026.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15787.1; -; Genomic_DNA.
DR PIR; JS0264; JS0264.
DR RefSeq; NP_416469.1; NC_000913.3.
DR RefSeq; WP_000786005.1; NZ_STEB01000050.1.
DR PDB; 1CW0; X-ray; 2.30 A; A=2-156.
DR PDB; 1ODG; X-ray; 2.80 A; A=23-156.
DR PDB; 1VSR; X-ray; 1.80 A; A=21-156.
DR PDBsum; 1CW0; -.
DR PDBsum; 1ODG; -.
DR PDBsum; 1VSR; -.
DR AlphaFoldDB; P09184; -.
DR SMR; P09184; -.
DR BioGRID; 4263264; 75.
DR BioGRID; 850827; 2.
DR DIP; DIP-11114N; -.
DR IntAct; P09184; 10.
DR STRING; 511145.b1960; -.
DR REBASE; 13373; V.EcoW3110DcmP.
DR REBASE; 175269; V.Rga4872ORF487P.
DR REBASE; 175272; V.Rga4872ORF19P.
DR REBASE; 232039; V.Sen4024DcmP.
DR REBASE; 232757; V.Sen4839DcmP.
DR REBASE; 3641; V.EcoKDcm.
DR PaxDb; P09184; -.
DR PRIDE; P09184; -.
DR EnsemblBacteria; AAC75026; AAC75026; b1960.
DR EnsemblBacteria; BAA15787; BAA15787; BAA15787.
DR GeneID; 946476; -.
DR KEGG; ecj:JW1943; -.
DR KEGG; eco:b1960; -.
DR PATRIC; fig|1411691.4.peg.292; -.
DR EchoBASE; EB1061; -.
DR eggNOG; COG3727; Bacteria.
DR HOGENOM; CLU_111913_1_1_6; -.
DR InParanoid; P09184; -.
DR OMA; HDCYLFK; -.
DR PhylomeDB; P09184; -.
DR BioCyc; EcoCyc:EG11068-MON; -.
DR EvolutionaryTrace; P09184; -.
DR PRO; PR:P09184; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0003677; F:DNA binding; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0043765; F:T/G mismatch-specific endonuclease activity; IDA:EcoCyc.
DR GO; GO:0006298; P:mismatch repair; IDA:EcoCyc.
DR CDD; cd00221; Vsr; 1.
DR InterPro; IPR004603; DNA_mismatch_endonuc_vsr.
DR InterPro; IPR011335; Restrct_endonuc-II-like.
DR Pfam; PF03852; Vsr; 1.
DR PIRSF; PIRSF018267; VSR_endonuc; 1.
DR SUPFAM; SSF52980; SSF52980; 1.
DR TIGRFAMs; TIGR00632; vsr; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; Endonuclease; Hydrolase; Magnesium;
KW Metal-binding; Nuclease; Reference proteome; Zinc.
FT CHAIN 1..156
FT /note="DNA mismatch endonuclease Vsr"
FT /id="PRO_0000200289"
FT BINDING 51
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 51
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 63
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT HELIX 7..15
FT /evidence="ECO:0007829|PDB:1CW0"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:1CW0"
FT HELIX 26..34
FT /evidence="ECO:0007829|PDB:1VSR"
FT STRAND 40..42
FT /evidence="ECO:0007829|PDB:1VSR"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:1VSR"
FT HELIX 55..57
FT /evidence="ECO:0007829|PDB:1VSR"
FT STRAND 59..64
FT /evidence="ECO:0007829|PDB:1VSR"
FT TURN 66..70
FT /evidence="ECO:0007829|PDB:1VSR"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:1VSR"
FT HELIX 83..106
FT /evidence="ECO:0007829|PDB:1VSR"
FT STRAND 110..115
FT /evidence="ECO:0007829|PDB:1VSR"
FT HELIX 116..119
FT /evidence="ECO:0007829|PDB:1VSR"
FT HELIX 127..139
FT /evidence="ECO:0007829|PDB:1VSR"
FT STRAND 144..148
FT /evidence="ECO:0007829|PDB:1VSR"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:1VSR"
SQ SEQUENCE 156 AA; 18016 MW; 24F98A111C31E098 CRC64;
MADVHDKATR SKNMRAIATR DTAIEKRLAS LLTGQGLAFR VQDASLPGRP DFVVDEYRCV
IFTHGCFWHH HHCYLFKVPA TRTEFWLEKI GKNVERDRRD ISRLQELGWR VLIVWECALR
GREKLTDEAL TERLEEWICG EGASAQIDTQ GIHLLA
