Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.22 kDa 
• Atom Count: 3067 
• Modelled Residue Count: 360 
• Deposited Residue Count: 369 
• Unique protein chains: 1

2F7V

Structure of acetylcitrulline deacetylase complexed with one Co

• PDB DOI: 10.2210/pdb2F7V/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas campestris
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-01 Released: 2006-09-26 
• Deposition Author(s): Shi, D., Yu, X., Roth, L., Allewell, N.M., Tuchman, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.225 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Structure of a novel N-acetyl-L-citrulline deacetylase from Xanthomonas campestris

Shi, D., Yu, X., Roth, L., Tuchman, M., Allewell, N.M.

(2007) Biophys Chem 126: 86-93

• PubMed: 16750290 
• DOI: 10.1016/j.bpc.2006.05.013
• Primary Citation of Related Structures:  
  2F7V, 2F8H


• PubMed Abstract: 
  

The structure of a novel acetylcitrulline deacetylase from the plant pathogen Xanthomonas campestris has been solved by multiple-wavelength anomalous dispersion (MAD) using crystals grown from selenomethionine-substituted protein and refined at 1.75 A resolution. The asymmetric unit of the crystal contains one monomer consisting of two domains, a catalytic domain and a dimerization domain. The catalytic domain is able to bind a single Co(II) ion at the active site with no change in conformation. The dimerization domain forms an interface between two monomers related by a crystallographic two-fold symmetry axis. The interface is maintained by hydrophobic interactions between helices and hydrogen bonding between two beta strands that form a continuous beta sheet across the dimer interface. Because the dimers are also related by two-fold crystallographic axes, they pack together across the crystal via the dimerization domain, suggesting that higher order oligomers may form in solution. The polypeptide fold of the monomer is similar to the fold of Pseudomonas sp. carboxypeptidase G2 and Neisseria meningitidis succinyl diaminopimelate desuccinylase. Structural comparison among these enzymes allowed modeling of substrate binding and suggests a possible catalytic mechanism, in which Glu130 functions as a bifunctional general acid-base catalyst and the metal ion polarizes the carbonyl of the acetyl group.

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Organizational Affiliation: 

Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, N.W., Washington, DC 20010-2970, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aectylcitrulline deacetylase	A	369	Xanthomonas campestris	Mutation(s): 0  EC: 3.5.1.16 (PDB Primary Data), 3.5.1 (UniProt)
UniProt
Find proteins for Q8P8J5 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P8J5  Go to UniProtKB:  Q8P8J5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.225 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.068	α = 90
b = 95.429	β = 93.77
c = 43.67	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-01 
• Released Date: 2006-09-26 
Deposition Author(s): Shi, D., Yu, X., Roth, L., Allewell, N.M., Tuchman, M.

Revision History  

• Version 1.0: 2006-09-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance