PDBsum entry 2oa9

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
246 a.a. *
225 a.a. *
ACT ×2
_CD ×15
_CL ×2
Waters ×288
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Restriction endonuclease mvai in the absence of DNA
Structure: R.Mvai. Chain: a, b. Engineered: yes
Source: Kocuria varians. Organism_taxid: 1272. Gene: mvair. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.50Å     R-factor:   0.186     R-free:   0.212
Authors: M.Kaus-Drobek,H.Czapinska,M.Sokolowska,G.Tamulaitis, R.H.Szczepanowski,K.Urbanke,V.Siksnys,M.Bochtler
Key ref: M.Kaus-Drobek et al. (2007). Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically. Nucleic Acids Res, 35, 2035-2046. PubMed id: 17344322
15-Dec-06     Release date:   20-Feb-07    
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Protein chain
Pfam   ArchSchema ?
Q8RNV5  (Q8RNV5_MICVA) -  R.MvaI
246 a.a.
246 a.a.
Protein chain
Pfam   ArchSchema ?
Q8RNV5  (Q8RNV5_MICVA) -  R.MvaI
246 a.a.
225 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  


Nucleic Acids Res 35:2035-2046 (2007)
PubMed id: 17344322  
Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.
M.Kaus-Drobek, H.Czapinska, M.SokoĊ‚owska, G.Tamulaitis, R.H.Szczepanowski, C.Urbanke, V.Siksnys, M.Bochtler.
Restriction endonuclease MvaI recognizes the sequence CC/WGG (W stands for A or T, '/' designates the cleavage site) and generates products with single nucleotide 5'-overhangs. The enzyme has been noted for its tolerance towards DNA modifications. Here, we report a biochemical characterization and crystal structures of MvaI in an apo-form and in a complex with target DNA at 1.5 A resolution. Our results show that MvaI is a monomer and recognizes its pseudosymmetric target sequence asymmetrically. The enzyme consists of two lobes. The catalytic lobe anchors the active site residues Glu36, Asp50, Glu55 and Lys57 and contacts the bases from the minor grove side. The recognition lobe mediates all major grove interactions with the bases. The enzyme in the crystal is bound to the strand with T at the center of the recognition sequence. The crystal structure with calcium ions and DNA mimics the prereactive state. MvaI shows structural similarities to BcnI, which cleaves the related sequence CC/SGG and to MutH enzyme, which is a component of the DNA repair machinery, and nicks one DNA strand instead of making a double-strand break.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21227928 G.Kostiuk, G.Sasnauskas, G.Tamulaitiene, and V.Siksnys (2011).
Degenerate sequence recognition by the monomeric restriction enzyme: single mutation converts BcnI into a strand-specific nicking endonuclease.
  Nucleic Acids Res, 39, 3744-3753.  
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
20693529 I.Stier, and A.Kiss (2010).
The type II restriction endonuclease MvaI has dual specificity.
  Nucleic Acids Res, 38, 8231-8238.  
20571089 M.Zaremba, A.Owsicka, G.Tamulaitis, G.Sasnauskas, L.S.Shlyakhtenko, A.Y.Lushnikov, Y.L.Lyubchenko, N.Laurens, B.van den Broek, G.J.Wuite, and V.Siksnys (2010).
DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.
  Nucleic Acids Res, 38, 7142-7154.  
20587501 T.Raskó, A.Dér, E.Klement, K.Slaska-Kiss, E.Pósfai, K.F.Medzihradszky, D.R.Marshak, R.J.Roberts, and A.Kiss (2010).
BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism.
  Nucleic Acids Res, 38, 7155-7166.  
19400796 M.Szczepek, P.Mackeldanz, E.Möncke-Buchner, J.Alves, D.H.Krüger, and M.Reuter (2009).
Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition.
  Mol Microbiol, 72, 1011-1021.  
18086711 G.Gasiunas, G.Sasnauskas, G.Tamulaitis, C.Urbanke, D.Razaniene, and V.Siksnys (2008).
Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family.
  Nucleic Acids Res, 36, 938-949.  
18456708 J.Orlowski, and J.M.Bujnicki (2008).
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
  Nucleic Acids Res, 36, 3552-3569.  
19014591 K.H.Kaminska, M.Kawai, M.Boniecki, I.Kobayashi, and J.M.Bujnicki (2008).
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site.
  BMC Struct Biol, 8, 48.  
17617640 G.Tamulaitis, M.Zaremba, R.H.Szczepanowski, M.Bochtler, and V.Siksnys (2007).
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
  Nucleic Acids Res, 35, 4792-4799.  
17407166 J.Kosinski, E.Kubareva, and J.M.Bujnicki (2007).
A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.
  Proteins, 68, 324-336.  
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