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Protein

Very short patch repair protein

Gene

vsr

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Deamination of 5-methylcytosine in DNA results in T/G mismatches. If unrepaired, these mismatches can lead to C-to-C transition mutations. The very short patch (VSP) repair process in E.coli counteracts the mutagenic process by repairing the mismatches in favor of the G-containing strand. This enzyme is an endonuclease that nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue that is mismatched to 2'-deoxyguanosine. The incision is mismatch-dependent and strand-specific.

Cofactori

Protein has several cofactor binding sites:
  • Mg2+Note: Binds 2 magnesium ions per subunit.
  • Zn2+Note: Binds 1 zinc ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi51 – 511Magnesium 1
Metal bindingi51 – 511Magnesium 2
Metal bindingi63 – 631Magnesium 1

GO - Molecular functioni

  • DNA binding Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW
  • T/G mismatch-specific endonuclease activity Source: EcoCyc

GO - Biological processi

  • mismatch repair Source: EcoCyc
  • nucleic acid phosphodiester bond hydrolysis Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG11068-MONOMER.
ECOL316407:JW1943-MONOMER.

Protein family/group databases

REBASEi3641. V.EcoKDcm.

Names & Taxonomyi

Protein namesi
Recommended name:
Very short patch repair protein (EC:3.1.-.-)
Alternative name(s):
DNA mismatch endonuclease
V.EcoKDcm
Vsr mismatch endonuclease
Gene namesi
Name:vsr
Ordered Locus Names:b1960, JW1943
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11068. vsr.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved
Chaini2 – 156155Very short patch repair proteinPRO_0000200289Add
BLAST

Proteomic databases

PaxDbiP09184.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
mutLP233673EBI-765033,EBI-554913

Protein-protein interaction databases

BioGridi4263264. 75 interactions.
DIPiDIP-11114N.
IntActiP09184. 10 interactions.
STRINGi511145.b1960.

Structurei

Secondary structure

1
156
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 159Combined sources
Beta strandi19 – 213Combined sources
Helixi26 – 349Combined sources
Beta strandi40 – 423Combined sources
Beta strandi51 – 544Combined sources
Helixi55 – 573Combined sources
Beta strandi59 – 646Combined sources
Turni66 – 705Combined sources
Beta strandi80 – 823Combined sources
Helixi83 – 10624Combined sources
Beta strandi110 – 1156Combined sources
Helixi116 – 1194Combined sources
Helixi127 – 13913Combined sources
Beta strandi144 – 1485Combined sources
Beta strandi151 – 1544Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CW0X-ray2.30A2-156[»]
1ODGX-ray2.80A23-156[»]
1VSRX-ray1.80A21-156[»]
ProteinModelPortaliP09184.
SMRiP09184. Positions 2-156.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP09184.

Family & Domainsi

Sequence similaritiesi

Belongs to the vsr family.Curated

Phylogenomic databases

eggNOGiENOG41090BB. Bacteria.
COG3727. LUCA.
HOGENOMiHOG000239922.
InParanoidiP09184.
KOiK07458.
OMAiHDCYLFK.
OrthoDBiEOG6VXFGP.
PhylomeDBiP09184.

Family and domain databases

Gene3Di3.40.960.10. 1 hit.
InterProiIPR004603. DNA_mismatch_endonuc_vsr.
IPR011335. Restrct_endonuc-II-like.
[Graphical view]
PfamiPF03852. Vsr. 1 hit.
[Graphical view]
PIRSFiPIRSF018267. VSR_endonuc. 1 hit.
SUPFAMiSSF52980. SSF52980. 1 hit.
TIGRFAMsiTIGR00632. vsr. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P09184-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADVHDKATR SKNMRAIATR DTAIEKRLAS LLTGQGLAFR VQDASLPGRP
60 70 80 90 100
DFVVDEYRCV IFTHGCFWHH HHCYLFKVPA TRTEFWLEKI GKNVERDRRD
110 120 130 140 150
ISRLQELGWR VLIVWECALR GREKLTDEAL TERLEEWICG EGASAQIDTQ

GIHLLA
Length:156
Mass (Da):18,016
Last modified:January 23, 2007 - v3
Checksum:i24F98A111C31E098
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X13330 Genomic DNA. Translation: CAA31707.1.
M32307 Unassigned DNA. Translation: AAA03724.1.
U00096 Genomic DNA. Translation: AAC75026.1.
AP009048 Genomic DNA. Translation: BAA15787.1.
PIRiJS0264.
RefSeqiNP_416469.1. NC_000913.3.
WP_000786005.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75026; AAC75026; b1960.
BAA15787; BAA15787; BAA15787.
GeneIDi946476.
KEGGiecj:JW1943.
eco:b1960.
PATRICi32119249. VBIEscCol129921_2039.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X13330 Genomic DNA. Translation: CAA31707.1.
M32307 Unassigned DNA. Translation: AAA03724.1.
U00096 Genomic DNA. Translation: AAC75026.1.
AP009048 Genomic DNA. Translation: BAA15787.1.
PIRiJS0264.
RefSeqiNP_416469.1. NC_000913.3.
WP_000786005.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CW0X-ray2.30A2-156[»]
1ODGX-ray2.80A23-156[»]
1VSRX-ray1.80A21-156[»]
ProteinModelPortaliP09184.
SMRiP09184. Positions 2-156.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263264. 75 interactions.
DIPiDIP-11114N.
IntActiP09184. 10 interactions.
STRINGi511145.b1960.

Protein family/group databases

REBASEi3641. V.EcoKDcm.

Proteomic databases

PaxDbiP09184.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75026; AAC75026; b1960.
BAA15787; BAA15787; BAA15787.
GeneIDi946476.
KEGGiecj:JW1943.
eco:b1960.
PATRICi32119249. VBIEscCol129921_2039.

Organism-specific databases

EchoBASEiEB1061.
EcoGeneiEG11068. vsr.

Phylogenomic databases

eggNOGiENOG41090BB. Bacteria.
COG3727. LUCA.
HOGENOMiHOG000239922.
InParanoidiP09184.
KOiK07458.
OMAiHDCYLFK.
OrthoDBiEOG6VXFGP.
PhylomeDBiP09184.

Enzyme and pathway databases

BioCyciEcoCyc:EG11068-MONOMER.
ECOL316407:JW1943-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP09184.
PROiP09184.

Family and domain databases

Gene3Di3.40.960.10. 1 hit.
InterProiIPR004603. DNA_mismatch_endonuc_vsr.
IPR011335. Restrct_endonuc-II-like.
[Graphical view]
PfamiPF03852. Vsr. 1 hit.
[Graphical view]
PIRSFiPIRSF018267. VSR_endonuc. 1 hit.
SUPFAMiSSF52980. SSF52980. 1 hit.
TIGRFAMsiTIGR00632. vsr. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the dcm locus of Escherichia coli K12."
    Hanck T., Gerwin N., Fritz H.-J.
    Nucleic Acids Res. 17:5844-5844(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene."
    Sohail A., Lieb M., Dar M., Bhagwat A.S.
    J. Bacteriol. 172:4214-4221(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease."
    Hennecke F., Kolmar H., Bruendi K., Fritz H.-J.
    Nature 353:776-778(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  7. "Recognition of GT mismatches by Vsr mismatch endonuclease."
    Fox K.R., Allinson S.L., Sahagun-Krause H., Brown T.
    Nucleic Acids Res. 28:2535-2540(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  8. "Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex."
    Tsutakawa S.E., Jingami H., Morikawa K.
    Cell 99:615-623(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
  9. "Crystallographic and functional studies of very short patch repair endonuclease."
    Tsutakawa S.E., Muto T., Kawate T., Jingami H., Kunishima N., Ariyoshi M., Kohda D., Nakagawa M., Morikawa K.
    Mol. Cell 3:621-628(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 22-157.

Entry informationi

Entry nameiVSR_ECOLI
AccessioniPrimary (citable) accession number: P09184
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: January 23, 2007
Last modified: April 13, 2016
This is version 143 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.