Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.30 kDa 
• Atom Count: 8659 
• Modelled Residue Count: 1046 
• Deposited Residue Count: 1050 
• Unique protein chains: 2

6C62

An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme.

• PDB DOI: 10.2210/pdb6C62/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp. ADP
• Mutation(s): No 


• Deposited: 2018-01-17 Released: 2018-03-21 
• Deposition Author(s): Peat, T.S., Esquirol, L., Wilding, M., Liu, J.W., French, N.G., Hartley, C.J., Hideki, O., Easton, C.J., Newman, J., Scott, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.191 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Literature

An unexpected vestigial protein complex reveals the evolutionary origins of ans-triazine catabolic enzyme.

Esquirol, L., Peat, T.S., Wilding, M., Liu, J.W., French, N.G., Hartley, C.J., Onagi, H., Nebl, T., Easton, C.J., Newman, J., Scott, C.

(2018) J Biol Chem 293: 7880-7891

• PubMed: 29523689 
• DOI: 10.1074/jbc.RA118.001996
• Primary Citation of Related Structures:  
  6C62, 6C6G


• PubMed Abstract: 
  

Cyanuric acid is a metabolic intermediate of s -triazines, such as atrazine (a common herbicide) and melamine (used in resins and plastics). Cyanuric acid is mineralized to ammonia and carbon dioxide by the soil bacterium Pseudomonas sp. strain ADP via three hydrolytic enzymes (AtzD, AtzE, and AtzF). Here, we report the purification and biochemical and structural characterization of AtzE. Contrary to previous reports, we found that AtzE is not a biuret amidohydrolase, but instead it catalyzes the hydrolytic deamination of 1-carboxybiuret. X-ray crystal structures of apo AtzE and AtzE bound with the suicide inhibitor phenyl phosphorodiamidate revealed that the AtzE enzyme complex consists of two independent molecules in the asymmetric unit. We also show that AtzE forms an α2β2 heterotetramer with a previously unidentified 68-amino acid-long protein (AtzG) encoded in the cyanuric acid mineralization operon from Pseudomonas sp. strain ADP. Moreover, we observed that AtzG is essential for the production of soluble, active AtzE and that this obligate interaction is a vestige of their shared evolutionary origin. We propose that AtzEG was likely recruited into the cyanuric acid-mineralizing pathway from an ancestral glutamine transamidosome that required protein-protein interactions to enforce the exclusion of solvent from the transamidation reaction.

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Organizational Affiliation: 

Synthetic Biology Future Science Platform, CSIRO Land and Water, Canberra, Australian Capital Territory 2601.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biuret hydrolase	A, B	457	Pseudomonas sp. ADP	Mutation(s): 0  Gene Names: atzE EC: 3.5.1.84 (PDB Primary Data), 3.5.1.131 (UniProt)
UniProt
Find proteins for Q936X3 (Pseudomonas sp. (strain ADP)) Explore Q936X3  Go to UniProtKB:  Q936X3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AtzG	C, D	68	Pseudomonas sp. ADP	Mutation(s): 0  Gene Names: atzG
UniProt
Find proteins for A0A384E126 (Pseudomonas sp. (strain ADP)) Explore A0A384E126  Go to UniProtKB:  A0A384E126

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth B], F [auth D], G [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.191 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.489	α = 90
b = 89.04	β = 101.89
c = 141.672	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-01-17 
• Released Date: 2018-03-21 
Deposition Author(s): Peat, T.S., Esquirol, L., Wilding, M., Liu, J.W., French, N.G., Hartley, C.J., Hideki, O., Easton, C.J., Newman, J., Scott, C.

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2018-05-30
  Changes: Data collection, Database references, Source and taxonomy, Structure summary