9C0W

AzrC from Bacillus pacificus ROC1 bound to malachite green


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.284 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Isolation, identification, and characterisation of the malachite green detoxifying bacterial strain Bacillus pacificus ROC1 and the azoreductase AzrC.

Bibi, S.Breeze, C.W.Jadoon, V.Fareed, A.Syed, A.Frkic, R.L.Zaffar, H.Ali, M.Zeb, I.Jackson, C.J.Naqvi, T.A.

(2025) Sci Rep 15: 3499-3499

  • DOI: https://doi.org/10.1038/s41598-024-84609-4
  • Primary Citation of Related Structures:  
    9C0W

  • PubMed Abstract: 

    Malachite green (MG) is used as a dye for materials such as wood, cotton, and nylon, and is used in aquaculture to prevent fungal and protozoan diseases. However, it is highly toxic, with carcinogenic, mutagenic, and teratogenic properties, resulting in bans worldwide. Despite this, MG is still frequently used in many countries due to its efficacy and economy. MG is persistent in the environment and so requires degradative intervention. In this work we isolated Bacillus pacificus ROC1 strain from a salt flat in Pakistan that had the ability to aerobically detoxify MG, as determined by bacterio- and phyto-toxicity assays. We demonstrate immobilized B. pacificus ROC1 can effectively detoxify MG, which highlights a potential method for its biodegradation. Genomic sequencing identified three candidate azo-reductases within B. pacificus ROC1 that could be responsible for the MG-degrading activity. These were cloned, expressed and purified from Escherichia coli, with one (AzrC), catalyzing the reduction of MG to leuco-MG in vitro. AzrC was crystallised and MG was captured within the active site in a Michaelis complex, providing structural insight into the reduction mechanism. Altogether, this work identifies a bacterium capable of aerobically degrading a major industrial pollutant and characterizes the molecular basis for this activity.


  • Organizational Affiliation

    Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FMN-dependent NADH:quinone oxidoreductase 3
A, B
231Bacillus pacificusMutation(s): 0 
Gene Names: azoR3BCE_2269
EC: 1.6.5 (PDB Primary Data), 1.7.1.17 (PDB Primary Data)
UniProt
Find proteins for Q738X4 (Bacillus cereus (strain ATCC 10987 / NRS 248))
Explore Q738X4 
Go to UniProtKB:  Q738X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ738X4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.284 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.133α = 90
b = 74.164β = 90
c = 135.543γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

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 MGRClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Database references