9J9J | pdb_00009j9j

Nitrophenol monooxygenase RsPNPA from Rhodococcus sp. 21391


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.282 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: in silico
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Literature

Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificity.

Yang, J.Lin, S.Li, W.Wang, X.Li, R.

(2025) Microb Cell Fact 24: 85-85

  • DOI: https://doi.org/10.1186/s12934-025-02712-1
  • Primary Citation of Related Structures:  
    9J9J

  • PubMed Abstract: 

    Bioremediation relying on highly efficient degrading bacteria constitutes a promising and sustainable avenue for controlling and reducing nitrophenol contamination in the environment. A thorough understanding of the bacterial degradation mechanism of nitrophenol is of paramount importance for supporting the development of efficient microbial remediation technology. In this study, a new bacterium, Rhodococcus sp. 21391, endowed with superior p-nitrophenol (PNP) degradation ability was obtained. Genomic and comparative proteomic analyses revealed that it utilizes the 1,2,4-benzenetriol (BT) pathway for PNP degradation. The catalytic properties of the two-component p-nitrophenol monooxygenase RsNcpAB from the strain were investigated in vitro. The enzyme exhibited a broad substrate selectivity, catalyzing the oxidation of various nitrophenols and halogenated phenols, with significant potential for further research and development. Additionally, the crystal structure of the oxidative component of p-nitrophenol monooxygenase, RsNcpA, was determined. Structural analysis and site-directed mutagenesis revealed that residues Arg100 and His293 in the active site play a crucial role in enzyme catalysis, and a catalytic mechanism model was subsequently proposed. This study reports a high-performance nitrophenol-degrading bacterium and enzyme, and reveals their mechanisms at the molecular level. These findings increase the understanding of the bacterial degradation of nitrophenol, thereby providing a crucial foundation for the development of efficient bioremediation technologies.


  • Organizational Affiliation
    • School of Life and Health Technology, Dongguan University of Technology, Dongguan, China. yangjian@dgut.edu.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component
A, B, C
536Rhodococcus sp. 21391Mutation(s): 0 
Gene Names: npcA
EC: 1.14.13.166 (PDB Primary Data), 1.14.13.29 (PDB Primary Data)
UniProt
Find proteins for Q6F4M8 (Rhodococcus opacus)
Explore Q6F4M8 
Go to UniProtKB:  Q6F4M8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6F4M8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.282 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.561α = 90
b = 149.561β = 90
c = 322.141γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release