7T2Z

The structure of Haemophilus influenzae Rd KW20 nitroreductase complexed with 1-methyl-5-nitroimidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biochemical and structural characterization of Haemophilus influenzae nitroreductase in metabolizing nitroimidazoles.

Liu, D.Wanniarachchi, T.N.Jiang, G.Seabra, G.Cao, S.Bruner, S.D.Ding, Y.

(2022) RSC Chem Biol 3: 436-446

  • DOI: https://doi.org/10.1039/d1cb00238d
  • Primary Citation of Related Structures:  
    7T2Z, 7T33

  • PubMed Abstract: 

    Nitroheterocycle antibiotics, particularly 5-nitroimidazoles, are frequently used for treating anaerobic infections. The antimicrobial activities of these drugs heavily rely on the in vivo bioactivation, mainly mediated by widely distributed bacterial nitroreductases (NTRs). However, the bioactivation can also lead to severe toxicities and drug resistance. Mechanistic understanding of NTR-mediated 5-nitroimidazole metabolism can potentially aid addressing these issues. Here, we report the metabolism of structurally diverse nitroimidazole drug molecules by a NTR from a human pathogen Haemophilus influenzae (HiNfsB). Our detailed bioinformatic analysis uncovered that HiNfsB represents a group of unexplored oxygen-insensitive NTRs. Biochemical characterization of the recombinant enzyme revealed that HiNfsB effectively metabolizes ten clinically used nitroimidazoles. Furthermore, HiNfsB generated not only canonical nitroreduction metabolites but also stable, novel dimeric products from three nitroimidazoles, whose structures were proposed based on the results of high resolution MS and tandem MS analysis. X-ray structural analysis of the enzyme coupled with site-directed mutagenesis identified four active site residues important to its catalysis and broad substrate scope. Finally, transient expression of HiNfsB sensitized an E. coli mutant strain to 5-nitroimidazoles under anaerobic conditions. Together, these results advance our understanding of the metabolism of nitroimidazole antibiotics mediated by a new NTR group and reinforce the research on the natural antibiotic resistome for addressing the antibiotic resistance crisis.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida Gainesville Florida 32610 USA yding@cop.ufl.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative NAD(P)H nitroreductase
A, B
233Haemophilus influenzae Rd KW20Mutation(s): 0 
Gene Names: HI_1278
EC: 1
UniProt
Find proteins for Q57431 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore Q57431 
Go to UniProtKB:  Q57431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57431
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
EIV (Subject of Investigation/LOI)
Query on EIV

Download Ideal Coordinates CCD File 
F [auth A]1-methyl-5-nitro-1H-imidazole
C4 H5 N3 O2
JLZXSFPSJJMRIX-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
G [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.315α = 90
b = 57.315β = 90
c = 121.007γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description