In silico structure-function analysis of E. cloacae nitroreductase

Proteins. 2012 Dec;80(12):2728-41. doi: 10.1002/prot.24157. Epub 2012 Sep 15.

Abstract

Reduction, catalyzed by the bacterial nitroreductases, is the quintessential first step in the biodegradation of a variety of nitroaromatic compounds from contaminated waters and soil. The Enterobacter cloacae nitroreductase (EcNR) enzyme is considered as a prospective biotechnological tool for bioremediation of hazardous nitroaromatic compounds. Using diverse computational methods, we obtain insights into the structural basis of activity and mechanism of its function. We have performed molecular dynamics simulation of EcNR in three different states (free EcNR in oxidized form, fully reduced EcNR with benzoate inhibitor and fully reduced EcNR with nitrobenzene) in explicit solvent and with full electrostatics. Principal Component Analysis (PCA) of the variance-covariance matrix showed that the complexed nitroreductase becomes more flexible overall upon complexation, particularly helix H6, in the vicinity of the binding site. A multiple sequence alignment was also constructed in order to examine positional constraints on substitution in EcNR. Five regions which are highly conserved within the flavin mononucleotide (FMN) binding site were identified. Obtained results and their implications for EcNR functioning are discussed, and new plausible mechanism has been proposed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Catalytic Domain
  • Computational Biology / methods
  • Enterobacter cloacae / enzymology*
  • Flavin Mononucleotide / chemistry
  • Flavin Mononucleotide / metabolism
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Nitrobenzenes / chemistry
  • Nitrobenzenes / metabolism
  • Nitroreductases / chemistry*
  • Nitroreductases / metabolism*
  • Principal Component Analysis
  • Sequence Alignment
  • Static Electricity
  • Structure-Activity Relationship

Substances

  • Bacterial Proteins
  • Nitrobenzenes
  • Flavin Mononucleotide
  • nitrobenzene
  • Nitroreductases