Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 22.19 kDa 
• Atom Count: 1629 
• Modelled Residue Count: 200 
• Deposited Residue Count: 200 
• Unique protein chains: 1

2D5I

The crystal structure of AzoR (Azo Reductase) from Escherichia coli

• PDB DOI: 10.2210/pdb2D5I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-11-02 Released: 2006-05-16 
• Deposition Author(s): Ito, K., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Three-dimensional structure of AzoR from Escherichia coli. An oxidereductase conserved in microorganisms

Ito, K., Nakanishi, M., Lee, W.C., Sasaki, H., Zenno, S., Saigo, K., Kitade, Y., Tanokura, M.

(2006) J Biol Chem 281: 20567-20576

• PubMed: 16684776 
• DOI: 10.1074/jbc.M513345200
• Primary Citation of Related Structures:  
  1V4B, 2D5I


• PubMed Abstract: 
  

The crystal structure of AzoR (azoreductase) has been determined in complex with FMN for two different crystal forms at 1.8 and 2.2 A resolution. AzoR is an oxidoreductase isolated from Escherichia coli as a protein responsible for the degradation of azo compounds. This enzyme is an FMN-dependent NADH-azoreductase and catalyzes the reductive cleavage of azo groups by a ping-pong mechanism. The structure suggests that AzoR acts in a homodimeric state forming the two identical catalytic sites to which both monomers contribute. The structure revealed that each monomer of AzoR has a flavodoxin-like structure, without the explicit overall amino acid sequence homology. Superposition of the structures from the two different crystal forms revealed the conformational change and suggested a mechanism for accommodating substrates of different size. Furthermore, comparison of the active site structure with that of NQO1 complexed with substrates provides clues to the possible substrate-binding mechanism of AzoR.

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Organizational Affiliation: 

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Azo Reductase	A	200	Escherichia coli K-12	Mutation(s): 0  Gene Names: azoR, acpD, b1412, JW1409 EC: 1.7.1.6 (PDB Primary Data), 1.6.5 (UniProt), 1.7.1.17 (UniProt)
UniProt
Find proteins for P41407 (Escherichia coli (strain K12)) Explore P41407  Go to UniProtKB:  P41407

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.63	α = 90
b = 94.63	β = 90
c = 54.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-02 
• Released Date: 2006-05-16 
Deposition Author(s): Ito, K., Tanokura, M.

Revision History  

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2007-09-19
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance