4BVR

Cyanuric acid hydrolase: evolutionary innovation by structural concatenation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1111/mmi.12249
  • Primary Citation of Related Structures:  3ZGR, 3ZGS, 3ZGT, 3ZGU, 4BVQ, 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 conc ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYANURIC ACID AMIDOHYDROLASE
A, B
383Pseudomonas sp. (strain ADP)Gene Names: atzD
EC: 3.5.2.15
Find proteins for P58329 (Pseudomonas sp. (strain ADP))
Go to UniProtKB:  P58329
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WDL
Query on WDL

Download SDF File 
Download CCD File 
A, B
1,3,5-triazine-2,4,6-triol
Cyanuric Acid
C3 H3 N3 O3
ZFSLODLOARCGLH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.176 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 129.075α = 90.00
b = 129.075β = 90.00
c = 229.660γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release