Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.23 kDa 
• Atom Count: 4398 
• Modelled Residue Count: 484 
• Deposited Residue Count: 530 
• Unique protein chains: 1

3UFB

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

• DOI: 10.2210/pdb3UFB/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio vulnificus YJ016
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-01 Released: 2012-11-07 
• Deposition Author(s): Park, S.Y., Lee, H.J., Sun, J., Nishi, K., Song, J.M., Kim, J.S.

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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 

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

• PubMed: 23090406 
• 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 (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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I restriction-modification system methyltransferase subunit	A	530	Vibrio vulnificus YJ016	Mutation(s): 0  Gene Names: VV0266 EC: 2.1.1.72
UniProt
Find proteins for Q7MPU6 (Vibrio vulnificus (strain YJ016)) Explore Q7MPU6  Go to UniProtKB:  Q7MPU6

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 = 78.899	α = 90
b = 78.899	β = 90
c = 165.802	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-01 
• Released Date: 2012-11-07 
Deposition Author(s): Park, S.Y., Lee, H.J., Sun, J., Nishi, K., Song, J.M., Kim, J.S.

Revision History  

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