2OA9

Restriction endonuclease MvaI in the absence of DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.

Kaus-Drobek, M.Czapinska, H.Sokolowska, M.Tamulaitis, G.Szczepanowski, R.H.Urbanke, C.Siksnys, V.Bochtler, M.

(2007) Nucleic Acids Res. 35: 2035-2046

  • DOI: 10.1093/nar/gkm064
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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. He ...

    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.


    Related Citations: 
    • Structural and Mechanistic Similarities between Restriction Endonucleases BcnI and MvaI and the DNA Repair Protein MutH.
      Sokolowska, M.,Kaus-Drobek, M.,Czapinska, H.,Tamulaitis, G.,Siksnys, V.,Bochtler, M.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    International Institute of Molecular and Cell Biology, Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
R.MvaI
A, B
249Kocuria variansMutation(s): 0 
Gene Names: mvaIR
Find proteins for Q8RNV5 (Kocuria varians)
Go to UniProtKB:  Q8RNV5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.499α = 90.00
b = 63.281β = 100.77
c = 71.892γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
NCSREFmodel building
SHELXDphasing
DMphasing
REFMACrefinement
ARP/wARPmodel building
SHARPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance