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: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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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 D Biol Crystallogr 68: 1570-1577

  • DOI: 10.1107/S0907444912038826
  • Primary Citation of Related Structures:  
    3UFB

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type I restriction-modification system methyltransferase subunitA530Vibrio vulnificus YJ016Mutation(s): 0 
Gene Names: VV0266
EC: 2.1.1.72
Find proteins for Q7MPU6 (Vibrio vulnificus (strain YJ016))
Explore Q7MPU6 
Go to UniProtKB:  Q7MPU6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.899α = 90
b = 78.899β = 90
c = 165.802γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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