PDBsum entry 1vsr

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protein metals links
Hydrolase PDB id
Protein chain
134 a.a. *
Waters ×63
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Very short patch repair (vsr) endonuclease from escherichia
Structure: Protein (vsr endonuclease). Chain: a. Fragment: fragment. Synonym: patch repair protein,DNA mismatch endonuclease. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: vsr. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: pcr
1.80Å     R-factor:   0.196     R-free:   0.216
Authors: S.E.Tsutakawa,T.Muto,H.Jingami,N.Kunishima,M.Ariyoshi,D.Kohd M.Nakagawa,K.Morikawa
Key ref:
S.E.Tsutakawa et al. (1999). Crystallographic and functional studies of very short patch repair endonuclease. Mol Cell, 3, 621-628. PubMed id: 10360178 DOI: 10.1016/S1097-2765(00)80355-X
13-Feb-99     Release date:   27-Oct-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P09184  (VSR_ECOLI) -  Very short patch repair protein
156 a.a.
134 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     mismatch repair   1 term 
  Biochemical function     endonuclease activity     1 term  


DOI no: 10.1016/S1097-2765(00)80355-X Mol Cell 3:621-628 (1999)
PubMed id: 10360178  
Crystallographic and functional studies of very short patch repair endonuclease.
S.E.Tsutakawa, T.Muto, T.Kawate, H.Jingami, N.Kunishima, M.Ariyoshi, D.Kohda, M.Nakagawa, K.Morikawa.
Vsr endonuclease plays a crucial role in the repair of TG mismatched base pairs, which are generated by the spontaneous degradation of methylated cytidines; Vsr recognizes the mismatched base pair and cleaves the phosphate backbone 5' to the thymidine. We have determined the crystal structure of a truncated form of this endonuclease at 1.8 A resolution. The protein contains one structural zinc-binding module. Unexpectedly, its overall topology resembles members of the type II restriction endonuclease family. Subsequent mutational and biochemical analyses showed that certain elements in the catalytic site are also conserved. However, the identification of a critical histidine and evidence of an active site metal-binding coordination that is novel to endonucleases indicate a distinct catalytic mechanism.
  Selected figure(s)  
Figure 3.
Figure 4.
Figure 4. Similarity of Topology to Restriction Type II Endonucleases(A–C) Ribbon diagrams of (A) Vsr, (B) one subunit of BamHI ([32]), and (C) one subunit of EcoRV ( [46]) after superimposition of the side chain of the first conserved aspartate in the conserved catalytic motif and overlaying β strands. Figures were derived from 1bhm and 1rvb. Side chains important for endonuclease activity are depicted. Carbon, oxygen, and nitrogen atoms are depicted in green, red, and blue, respectively.(D) Enlarged view of superimposed Vsr (blue), BamHI (brown), and EcoRV (green) active sites, with side chains from the active site motif displayed.
  The above figures are reprinted by permission from Cell Press: Mol Cell (1999, 3, 621-628) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20511499 A.Kwiatek, M.Luczkiewicz, K.Bandyra, D.C.Stein, and A.Piekarowicz (2010).
Neisseria gonorrhoeae FA1090 carries genes encoding two classes of Vsr endonucleases.
  J Bacteriol, 192, 3951-3960.  
  20725617 K.Fukui (2010).
DNA mismatch repair in eukaryotes and bacteria.
  J Nucleic Acids, 2010, 0.  
20375162 S.K.Menon, B.J.Eilers, M.J.Young, and C.M.Lawrence (2010).
The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily.
  J Virol, 84, 5890-5897.
PDB code: 2w8m
17623842 C.R.Guzzo, R.A.Nagem, J.A.Barbosa, and C.S.Farah (2007).
Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif.
  Proteins, 69, 644-651.
PDB code: 2g3w
17214552 L.Mones, I.Simon, and M.Fuxreiter (2007).
Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
  Biol Chem, 388, 73-78.  
16873236 K.Hara, F.I.Schmidt, M.Crow, and G.G.Brownlee (2006).
Amino acid residues in the N-terminal region of the PA subunit of influenza A virus RNA polymerase play a critical role in protein stability, endonuclease activity, cap binding, and virion RNA promoter binding.
  J Virol, 80, 7789-7798.  
16537396 V.V.Kapitonov, and J.Jurka (2006).
Self-synthesizing DNA transposons in eukaryotes.
  Proc Natl Acad Sci U S A, 103, 4540-4545.  
15985153 D.J.Rigden (2005).
An inactivated nuclease-like domain in RecC with novel function: implications for evolution.
  BMC Struct Biol, 5, 9.  
16011798 J.Kosinski, M.Feder, and J.M.Bujnicki (2005).
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.
  BMC Bioinformatics, 6, 172.  
15972856 L.N.Kinch, K.Ginalski, L.Rychlewski, and N.V.Grishin (2005).
Identification of novel restriction endonuclease-like fold families among hypothetical proteins.
  Nucleic Acids Res, 33, 3598-3605.  
15720711 M.Feder, and J.M.Bujnicki (2005).
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.
  BMC Genomics, 6, 21.  
12519752 K.L.Carrick, and M.D.Topal (2003).
Amino acid substitutions at position 43 of NaeI endonuclease. Evidence for changes in NaeI structure.
  J Biol Chem, 278, 9733-9739.  
12655008 M.Laging, E.Lindner, H.J.Fritz, and W.Kramer (2003).
Repair of hydrolytic DNA deamination damage in thermophilic bacteria: cloning and characterization of a Vsr endonuclease homolog from Bacillus stearothermophilus.
  Nucleic Acids Res, 31, 1913-1920.  
14576294 M.Mucke, D.H.Kruger, and M.Reuter (2003).
Diversity of type II restriction endonucleases that require two DNA recognition sites.
  Nucleic Acids Res, 31, 6079-6084.  
12067333 A.S.Bhagwat, and M.Lieb (2002).
Cooperation and competition in mismatch repair: very short-patch repair and methyl-directed mismatch repair in Escherichia coli.
  Mol Microbiol, 44, 1421-1428.  
12142452 M.Fuxreiter, and I.Simon (2002).
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
  Protein Sci, 11, 1978-1983.  
12356742 M.Mücke, G.Grelle, J.Behlke, R.Kraft, D.H.Krüger, and M.Reuter (2002).
EcoRII: a restriction enzyme evolving recombination functions?
  EMBO J, 21, 5262-5268.  
12399478 N.Takahashi, Y.Naito, N.Handa, and I.Kobayashi (2002).
A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex.
  J Bacteriol, 184, 6100-6108.  
12361800 Y.W.Kow (2002).
Repair of deaminated bases in DNA.
  Free Radic Biol Med, 33, 886-893.  
11557809 S.E.Tsutakawa, and K.Morikawa (2001).
The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.
  Nucleic Acids Res, 29, 3775-3783.  
10911996 A.B.Hickman, Y.Li, S.V.Mathew, E.W.May, N.L.Craig, and F.Dyda (2000).
Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
  Mol Cell, 5, 1025-1034.
PDB code: 1f1z
10871403 K.R.Fox, S.L.Allinson, H.Sahagun-Krause, and T.Brown (2000).
Recognition of GT mismatches by Vsr mismatch endonuclease.
  Nucleic Acids Res, 28, 2535-2540.  
10856254 Q.Huai, J.D.Colandene, Y.Chen, F.Luo, Y.Zhao, M.D.Topal, and H.Ke (2000).
Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.
  EMBO J, 19, 3110-3118.
PDB code: 1ev7
10607611 I.Kobayashi, A.Nobusato, N.Kobayashi-Takahashi, and I.Uchiyama (1999).
Shaping the genome--restriction-modification systems as mobile genetic elements.
  Curr Opin Genet Dev, 9, 649-656.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.