4NQ3

Crystal structure of cyanuic acid hydrolase from A. caulinodans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cyanuric acid hydrolase from Azorhizobium caulinodans ORS 571: crystal structure and insights into a new class of Ser-Lys dyad proteins.

Cho, S.Shi, K.Seffernick, J.L.Dodge, A.G.Wackett, L.P.Aihara, H.

(2014) PLoS One 9: e99349-e99349

  • DOI: 10.1371/journal.pone.0099349
  • Primary Citation of Related Structures:  
    4NQ3

  • PubMed Abstract: 
  • Cyanuric acid hydrolase (CAH) catalyzes the hydrolytic ring-opening of cyanuric acid (2,4,6-trihydroxy-1,3,5-triazine), an intermediate in s-triazine bacterial degradation and a by-product from disinfection with trichloroisocyanuric acid. In the present study, an X-ray crystal structure of the CAH-barbituric acid inhibitor complex from Azorhizobium caulinodans ORS 571 has been determined at 2 ...

    Cyanuric acid hydrolase (CAH) catalyzes the hydrolytic ring-opening of cyanuric acid (2,4,6-trihydroxy-1,3,5-triazine), an intermediate in s-triazine bacterial degradation and a by-product from disinfection with trichloroisocyanuric acid. In the present study, an X-ray crystal structure of the CAH-barbituric acid inhibitor complex from Azorhizobium caulinodans ORS 571 has been determined at 2.7 Å resolution. The CAH protein fold consists of three structurally homologous domains forming a β-barrel-like structure with external α-helices that result in a three-fold symmetry, a dominant feature of the structure and active site that mirrors the three-fold symmetrical shape of the substrate cyanuric acid. The active site structure of CAH is similar to that of the recently determined AtzD with three pairs of active site Ser-Lys dyads. In order to determine the role of each Ser-Lys dyad in catalysis, a mutational study using a highly sensitive, enzyme-coupled assay was conducted. The 10⁹-fold loss of activity by the S226A mutant was at least ten times lower than that of the S79A and S333A mutants. In addition, bioinformatics analysis revealed the Ser226/Lys156 dyad as the only absolutely conserved dyad in the CAH/barbiturase family. These data suggest that Lys156 activates the Ser226 nucleophile which can then attack the substrate carbonyl. Our combination of structural, mutational, and bioinformatics analyses differentiates this study and provides experimental data for mechanistic insights into this unique protein family.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyanuric acid amidohydrolaseA, B356Azorhizobium caulinodans ORS 571Mutation(s): 0 
Gene Names: AZC_3892
EC: 3.5.2.15
Find proteins for A8IKD2 (Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / JCM 20966 / NBRC 14845 / NCIMB 13405 / ORS 571))
Explore A8IKD2 
Go to UniProtKB:  A8IKD2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR8
Query on BR8

Download Ideal Coordinates CCD File 
C [auth A], J [auth A], M [auth B]BARBITURIC ACID
C4 H4 N2 O3
HNYOPLTXPVRDBG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , N [auth B] , O [auth B] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  N [auth B],  O [auth B],  P [auth B],  Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth A], L [auth A], R [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 237.866α = 90
b = 237.866β = 90
c = 105.313γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release