Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 68077.24 
• Atom Count: 4176 
• Residue Count: 590 
• Unique protein chains: 1

3H1T

The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016

• DOI: 10.2210/pdb3H1T/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio vulnificus (strain YJ016)
• Expression System: Escherichia coli


• Deposited: 2009-04-13 Released: 2009-10-20 
• Deposition Author(s): Park, S.Y., Lee, H.J., Kim, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.242 
• R-Value Work: 0.218 

Literature

The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity

Uyen, N.T., Park, S.Y., Choi, J.W., Lee, H.J., Nishi, K., Kim, J.S.

(2009) Nucleic Acids Res. --: --

• PubMed: 19625490 
• DOI: 10.1093/nar/gkp603


• PubMed Abstract: 
  

Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its methylation status, type I enzymes composed of three subunits are interesting because of their unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR). The elucidated N-terminal fragment structure of a putative HsdR subunit from Vibrio vulnificus YJ016 reveals three globular domains. The nucleolytic core within an N-terminal nuclease domain (NTD) is composed of one basic and three acidic residues, which include a metal-binding site. An ATP hydrolase (ATPase) site at the interface of two RecA-like domains (RDs) is located close to the probable DNA-binding site for translocation, which is far from the NTD nucleolytic core. Comparison of relative domain arrangements with other functionally related ATP and/or DNA complex structures suggests a possible translocation and restriction mechanism of the HsdR subunit. Furthermore, careful analysis of its sequence and structure implies that a linker helix connecting two RDs and an extended region within the nuclease domain may play a central role in switching the DNA translocation into the restriction activity.

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Organizational Affiliation: 

Interdisciplinary Graduate Program in Molecular Medicine, Gwangju 501-746, Korea.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Type I site-specific restriction-modification system, R (Restriction) subunit	A	590	Vibrio vulnificus (strain YJ016)	Mutation(s): 0
Find proteins for Q7MPU7 (Vibrio vulnificus (strain YJ016)) Go to UniProtKB:  Q7MPU7

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.242 
• R-Value Work: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 71.244	α = 90.00
b = 88.780	β = 90.00
c = 114.227	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-04-13 
• Released Date: 2009-10-20 
• Deposition Author(s): Park, S.Y., Lee, H.J., Kim, J.S.

Revision History 

• Version 1.0: 2009-10-20
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance