RCSB PDB - 3W78: Crystal Structure of azoreductase AzrC in complex with NAD(P)-inhibitor Cibacron Blue

 3W78

Crystal Structure of azoreductase AzrC in complex with NAD(P)-inhibitor Cibacron Blue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Structures of AzrA and of AzrC complexed with substrate or inhibitor: insight into substrate specificity and catalytic mechanism.

Yu, J.Ogata, D.Gai, Z.Taguchi, S.Tanaka, I.Ooi, T.Yao, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 553-564

  • DOI: https://doi.org/10.1107/S1399004713030988
  • Primary Citation of Related Structures:  
    3W77, 3W78, 3W79, 3W7A

  • PubMed Abstract: 

    Azo dyes are major synthetic dyestuffs with one or more azo bonds and are widely used for various industrial purposes. The biodegradation of residual azo dyes via azoreductase-catalyzed cleavage is very efficient as the initial step of wastewater treatment. The structures of the complexes of azoreductases with various substrates are therefore indispensable to understand their substrate specificity and catalytic mechanism. In this study, the crystal structures of AzrA and of AzrC complexed with Cibacron Blue (CB) and the azo dyes Acid Red 88 (AR88) and Orange I (OI) were determined. As an inhibitor/analogue of NAD(P)H, CB was located on top of flavin mononucleotide (FMN), suggesting a similar binding manner as NAD(P)H for direct hydride transfer to FMN. The structures of the AzrC-AR88 and AzrC-OI complexes showed two manners of binding for substrates possessing a hydroxy group at the ortho or the para position of the azo bond, respectively, while AR88 and OI were estimated to have a similar binding affinity to AzrC from ITC experiments. Although the two substrates were bound in different orientations, the hydroxy groups were located in similar positions, resulting in an arrangement of electrophilic C atoms binding with a proton/electron-donor distance of ∼3.5 Å to N5 of FMN. Catalytic mechanisms for different substrates are proposed based on the crystal structures and on site-directed mutagenesis analysis.


  • Organizational Affiliation

    Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FMN-dependent NADH-azoreductaseA,
B [auth D],
C [auth B],
D [auth C]
211Bacillus sp. B29Mutation(s): 0 
Gene Names: azrCazoR
EC: 1.7 (PDB Primary Data), 1.6.5 (UniProt), 1.7.1.17 (UniProt)
UniProt
Find proteins for C0STY1 (Bacillus sp. B29)
Explore C0STY1 
Go to UniProtKB:  C0STY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0STY1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CBD
Query on CBD

Download Ideal Coordinates CCD File 
F [auth A],
H [auth D],
J [auth B],
L [auth C]
CIBACRON BLUE
C29 H20 Cl N7 O11 S3
YKCWQPZFAFZLBI-UHFFFAOYSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth D],
I [auth B],
K [auth C]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.37α = 90
b = 146.37β = 90
c = 116.2γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CBDClick on this verticalbar to view detailsBest fitted FMNClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2019-12-25
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description