4CP8

Structure of the amidase domain of allophanate hydrolase from Pseudomonas sp strain ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-Ray Structure of the Amidase Domain of Atzf, the Allophanate Hydrolase from the Cyanuric Acid-Mineralizing Multienzyme Complex.

Balotra, S.Newman, J.Cowieson, N.P.French, N.G.Campbell, P.M.Briggs, L.J.Warden, A.C.Easton, C.J.Peat, T.S.Scott, C.

(2015) Appl.Environ.Microbiol. 81: 470

  • DOI: 10.1128/AEM.02783-14

  • PubMed Abstract: 
  • The activity of the allophanate hydrolase from Pseudomonas sp. strain ADP, AtzF, provides the final hydrolytic step for the mineralization of s-triazines, such as atrazine and cyanuric acid. Indeed, the action of AtzF provides metabolic access to two ...

    The activity of the allophanate hydrolase from Pseudomonas sp. strain ADP, AtzF, provides the final hydrolytic step for the mineralization of s-triazines, such as atrazine and cyanuric acid. Indeed, the action of AtzF provides metabolic access to two of the three nitrogens in each triazine ring. The X-ray structure of the N-terminal amidase domain of AtzF reveals that it is highly homologous to allophanate hydrolases involved in a different catabolic process in other organisms (i.e., the mineralization of urea). The smaller C-terminal domain does not appear to have a physiologically relevant catalytic function, as reported for the allophanate hydrolase of Kluyveromyces lactis, when purified enzyme was tested in vitro. However, the C-terminal domain does have a function in coordinating the quaternary structure of AtzF. Interestingly, we also show that AtzF forms a large, ca. 660-kDa, multienzyme complex with AtzD and AtzE that is capable of mineralizing cyanuric acid. The function of this complex may be to channel substrates from one active site to the next, effectively protecting unstable metabolites, such as allophanate, from solvent-mediated decarboxylation to a dead-end metabolic product.


    Organizational Affiliation

    CSIRO Biomedical Manufacturing Program, Parkville, VIC, Australia.,Australian Synchrotron, Clayton, VIC, Australia.,Research School of Chemistry, Australian National University, Canberra, ACT, Ausralia.,CSIRO Land and Water Flagship, Black Mountain, Canberra, ACT, Australia colin.scott@csiro.au.,CSIRO Land and Water Flagship, Black Mountain, Canberra, ACT, Australia Research School of Chemistry, Australian National University, Canberra, ACT, Ausralia.,CSIRO Land and Water Flagship, Black Mountain, Canberra, ACT, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALLOPHANATE HYDROLASE
A, B, C, D, E, F
487Pseudomonas sp. (strain ADP)Mutation(s): 0 
Gene Names: atzF
EC: 3.5.1.54
Find proteins for Q936X2 (Pseudomonas sp. (strain ADP))
Go to UniProtKB:  Q936X2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download SDF File 
Download CCD File 
A, B, C, D
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.447α = 90.00
b = 179.232β = 106.63
c = 112.610γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2015-01-21
    Type: Database references