5AKQ | pdb_00005akq

X-ray structure and mutagenesis studies of the N-isopropylammelide isopropylaminohydrolase, AtzC

• PDB DOI: https://doi.org/10.2210/pdb5AKQ/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp. ADP
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-03-05 Released: 2015-03-18 
• Deposition Author(s): Balotra, S., Warden, A.C., Newman, J., Briggs, L.J., Scott, C., Peat, T.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

X-Ray Structure and Mutagenesis Studies of the N-Isopropylammelide Isopropylaminohydrolase, Atzc

Balotra, S., Warden, A.C., Newman, J., Briggs, L.J., Scott, C., Peat, T.S.

(2015) PLoS One 1: 37700

• PubMed: 26390431 
• DOI: https://doi.org/10.1371/journal.pone.0137700
• Primary Citation Related Structures: 
  4CQB, 4CQC, 4CQD, 5AKQ


• PubMed Abstract: 
  

  The N-isopropylammelide isopropylaminohydrolase from Pseudomonas sp. strain ADP, AtzC, provides the third hydrolytic step in the mineralization of s-triazine herbicides, such as atrazine. We obtained the X-ray crystal structure of AtzC at 1.84 Å with a weak inhibitor bound in the active site and then used a combination of in silico docking and site-directed mutagenesis to understand the interactions between AtzC and its substrate, isopropylammelide. The substitution of an active site histidine residue (His249) for an alanine abolished the enzyme's catalytic activity. We propose a plausible catalytic mechanism, consistent with the biochemical and crystallographic data obtained that is similar to that found in carbonic anhydrase and other members of subtype III of the amidohydrolase family.

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Organizational Affiliation: 
• CSIRO Land and Water Flagship, Black Mountain, Canberra, Australia; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.
CSIRO Land and Water Flagship, Black Mountain, Canberra, Australia.
CSIRO Biomedical Manufacturing, Parkville, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.54 kDa 
• Atom Count: 6,314 
• Modeled Residue Count: 800 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE	A, B	423	Pseudomonas sp. ADP	Mutation(s): 1  EC: 3.5.99.4 (PDB Primary Data), 3.5.4.42 (UniProt)
UniProt
Find proteins for O52063 (Pseudomonas sp. (strain ADP)) Explore O52063  Go to UniProtKB:  O52063

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.204	α = 90
b = 86.581	β = 104.36
c = 114.066	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Balotra, S., Warden, A.C., Newman, J., Briggs, L.J., Scott, C., Peat, T.S.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Database references
• Version 1.2: 2015-10-07
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description