RegulonDB RegulonDB 10.9: Gene Form
   

vsr gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dcm yedA yedI yedJ vsr terminator TSS_2276 TSS_2276 yedIp2 yedIp2 TSS_2275 TSS_2275 TSS_2274 (cluster) TSS_2274 (cluster) yedIp3 yedIp3 yodCp6 yodCp6

Gene      
Name: vsr    Texpresso search in the literature
Synonym(s): ECK1958, EG11068, b1960
Genome position(nucleotides): 2030448 <-- 2030918 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
56.05
External database links:  
ASAP:
ABE-0006507
CGSC:
28927
ECHOBASE:
EB1061
ECOLIHUB:
vsr
OU-MICROARRAY:
b1960
STRING:
511145.b1960
COLOMBOS: vsr


Product      
Name: DNA mismatch endonuclease Vsr
Synonym(s): DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway, Vsr
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 18.016
Isoelectric point: 7.541
Motif(s):
 
Type Positions Sequence
2 -> 74 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCY

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0043765 - T/G mismatch-specific endonuclease activity
biological_process GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0006298 - mismatch repair
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
Note(s): Note(s): ...[more].
Evidence: [APPHINH] Assay of protein purified to homogeneity from its native host
Reference(s): [1] Aravind L., et al., 2000
[2] Gabbara S., et al., 1994
[3] Glasner W., et al., 1992
[4] Hennecke F., et al., 1991
[5] Lieb M., et al., 2001
[6] Polosina YY., et al., 2009
[7] Takahashi N., et al., 2002
External database links:  
DIP:
DIP-11114N
ECOCYC:
EG11068-MONOMER
ECOLIWIKI:
b1960
INTERPRO:
IPR011335
INTERPRO:
IPR004603
MODBASE:
P09184
PDB:
1VSR
PDB:
1ODG
PDB:
1CW0
PFAM:
PF03852
PRIDE:
P09184
PRODB:
PRO_000024213
REFSEQ:
NP_416469
SMR:
P09184
UNIPROT:
P09184


Operon      
Name: dcm-vsr         
Operon arrangement:
Transcription unit        Promoter
dcm-vsr


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter yodCp6 2028504 reverse Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter yedIp3 2029370 reverse Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter TSS_2274 (cluster) 2029390 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [9]
  promoter TSS_2275 2029392 reverse nd [RS-EPT-CBR] [9]
  promoter yedIp2 2029461 reverse Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter TSS_2276 2031452 reverse nd [RS-EPT-CBR] [9]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Aravind L., Makarova KS., Koonin EV., 2000, SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories., Nucleic Acids Res 28(18):3417-32

 [2] Gabbara S., Wyszynski M., Bhagwat AS., 1994, A DNA repair process in Escherichia coli corrects U:G and T:G mismatches to C:G at sites of cytosine methylation., Mol Gen Genet 243(2):244-8

 [3] Glasner W., Merkl R., Schmidt S., Cech D., Fritz HJ., 1992, Fast quantitative assay of sequence-specific endonuclease activity based on DNA sequencer technology., Biol Chem Hoppe Seyler 373(12):1223-5

 [4] Hennecke F., Kolmar H., Brundl K., Fritz HJ., 1991, The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease., Nature 353(6346):776-8

 [5] Lieb M., Rehmat S., Bhagwat AS., 2001, Interaction of MutS and Vsr: some dominant-negative mutS mutations that disable methyladenine-directed mismatch repair are active in very-short-patch repair., J Bacteriol 183(21):6487-90

 [6] Polosina YY., Cupples CG., 2009, Changes in the conformation of the Vsr endonuclease amino-terminal domain accompany DNA cleavage., J Biochem 146(4):523-6

 [7] Takahashi N., Naito Y., Handa N., Kobayashi I., 2002, A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex., J Bacteriol 184(22):6100-8

 [8] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [9] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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