4BVT

Cyanuric acid hydrolase: evolutionary innovation by structural concatenation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cyanuric Acid Hydrolase: Evolutionary Innovation by Structural Concatenation.

Peat, T.S.Balotra, S.Wilding, M.French, N.G.Briggs, L.J.Panjikar, S.Cowieson, N.Newman, J.Scott, C.

(2013) Mol Microbiol 88: 1149

  • DOI: https://doi.org/10.1111/mmi.12249
  • Primary Citation of Related Structures:  
    4BVQ, 4BVR, 4BVS, 4BVT

  • PubMed Abstract: 

    The cyanuric acid hydrolase, AtzD, is the founding member of a newly identified family of ring-opening amidases. We report the first X-ray structure for this family, which is a novel fold (termed the 'Toblerone' fold) that likely evolved via the concatenation of monomers of the trimeric YjgF superfamily and the acquisition of a metal binding site. Structures of AtzD with bound substrate (cyanuric acid) and inhibitors (phosphate, barbituric acid and melamine), along with mutagenesis studies, allowed the identification of the active site. The AtzD monomer, active site and substrate all possess threefold rotational symmetry, to the extent that the active site possesses three potential Ser-Lys catalytic dyads. A single catalytic dyad (Ser85-Lys42) is hypothesized, based on biochemical evidence and crystallographic data. A plausible catalytic mechanism based on these observations is also presented. A comparison with a homology model of the related barbiturase, Bar, was used to infer the active-site residues responsible for substrate specificity, and the phylogeny of the 68 AtzD-like enzymes in the database were analysed in light of this structure-function relationship.


  • Organizational Affiliation

    CSIRO Materials, Science and Engineering, Parkville, Vic., 3801, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYANURIC ACID AMIDOHYDROLASE
A, B
383Pseudomonas sp. ADPMutation(s): 0 
EC: 3.5.2.15
UniProt
Find proteins for P58329 (Pseudomonas sp. (strain ADP))
Explore P58329 
Go to UniProtKB:  P58329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58329
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.23α = 90
b = 129.23β = 90
c = 233.791γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Data collection
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description