Structure of acetylcitrulline deacetylase from Xanthomonas campestris in metal-free form

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

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This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/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.

  • Organizational Affiliation

    Children's Research Institute, Children's National Medical Center, 111 Michigan Avenue, N.W., Washington, DC 20010-2970, USA. dshi@cnmcresearch.org

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
aectylcitrulline deacetylase369Xanthomonas campestrisMutation(s): 0 
EC: (PDB Primary Data), 3.5.1 (UniProt)
Find proteins for A0A0H2X6W0 (Xanthomonas campestris pv. campestris (strain 8004))
Explore A0A0H2X6W0 
Go to UniProtKB:  A0A0H2X6W0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2X6W0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.133α = 90
b = 95.226β = 93.76
c = 43.613γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description