3KEG | pdb_00003keg

X-ray Crystallographic Structure of a Y131F mutant of Pseudomonas Aeruginosa Azoreductase in complex with Methyl RED

• PDB DOI: https://doi.org/10.2210/pdb3KEG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-10-26 Released: 2010-01-12 
• Deposition Author(s): Wang, C.-J., Laurieri, N., Abuhammad, A., Lowe, E., Westwood, I., Ryan, A., Sim, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.210 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Role of tyrosine 131 in the active site of paAzoR1, an azoreductase with specificity for the inflammatory bowel disease prodrug balsalazide

Wang, C.-J., Laurieri, N., Abuhammad, A., Lowe, E., Westwood, I., Ryan, A., Sim, E.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 2-7

• PubMed: 20057057 
• DOI: https://doi.org/10.1107/S1744309109044741
• Primary Citation Related Structures: 
  3KEG


• PubMed Abstract: 
  

  Azoreductase 1 from Pseudomonas aeruginosa strain PAO1 (paAzoR1) catalyses the activation of the prodrug balsalazide and reduces the azo dye methyl red using reduced nicotinamide adenine dinucleotide cofactor as an electron donor. To investigate the mechanism of the enzyme, a Y131F mutation was introduced and the enzymic properties of the mutant were compared with those of the wild-type enzyme. The crystallographic structure of the mutant with methyl red bound was solved at 2.1 A resolution and compared with the wild-type structure. Tyr131 is important in the architecture of the active site but is not essential for enzymic activity.

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Organizational Affiliation: 
• Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, England.

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.67 kDa 
• Atom Count: 3,495 
• Modeled Residue Count: 398 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-dependent NADH-azoreductase 1	A, B	212	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: PA0785 EC: 1.7 (PDB Primary Data), 1.6.5 (UniProt), 1.7.1.17 (UniProt)
UniProt
Find proteins for Q9I5F3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5F3  Go to UniProtKB:  Q9I5F3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], G [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
MRE	D [auth A], E [auth A]	2-(4-DIMETHYLAMINOPHENYL)DIAZENYLBENZOIC ACID C15 H15 N3 O2 CEQFOVLGLXCDCX-WUKNDPDISA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.210 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.81	α = 90
b = 82.81	β = 90
c = 108.91	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Wang, C.-J., Laurieri, N., Abuhammad, A., Lowe, E., Westwood, I., Ryan, A., Sim, E.

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description