3UFB

Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016

Park, S.Y.Lee, H.J.Song, J.M.Sun, J.Hwang, H.J.Nishi, K.Kim, J.S.

(2012) Acta Crystallogr.,Sect.D 68: 1570-1577

  • DOI: 10.1107/S0907444912038826

  • PubMed Abstract: 
  • In multifunctional type I restriction enzymes, active methyltransferases (MTases) are constituted of methylation (HsdM) and specificity (HsdS) subunits. In this study, the crystal structure of a putative HsdM subunit from Vibrio vulnificus YJ016 (vvH ...

    In multifunctional type I restriction enzymes, active methyltransferases (MTases) are constituted of methylation (HsdM) and specificity (HsdS) subunits. In this study, the crystal structure of a putative HsdM subunit from Vibrio vulnificus YJ016 (vvHsdM) was elucidated at a resolution of 1.80 Å. A cofactor-binding site for S-adenosyl-L-methionine (SAM, a methyl-group donor) is formed within the C-terminal domain of an α/β-fold, in which a number of residues are conserved, including the GxGG and (N/D)PP(F/Y) motifs, which are likely to interact with several functional moieties of the SAM methyl-group donor. Comparison with the N6 DNA MTase of Thermus aquaticus and other HsdM structures suggests that two aromatic rings (Phe199 and Phe312) in the motifs that are conserved among the HsdMs may sandwich both sides of the adenine ring of the recognition sequence so that a conserved Asn residue (Asn309) can interact with the N6 atom of the target adenine base (a methyl-group acceptor) and locate the target adenine base close to the transferred SAM methyl group.


    Organizational Affiliation

    Department of Chemistry, Chonnam National University, Gwangju 500-757, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type I restriction-modification system methyltransferase subunit
A
530Vibrio vulnificus (strain YJ016)Mutation(s): 0 
Find proteins for Q7MPU6 (Vibrio vulnificus (strain YJ016))
Go to UniProtKB:  Q7MPU6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.899α = 90.00
b = 78.899β = 90.00
c = 165.802γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release