7T2Z

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

Summary for 7T2Z

• Entry DOI: 10.2210/pdb7t2z/pdb
• Descriptor: Putative NAD(P)H nitroreductase, 1,2-ETHANEDIOL, FLAVIN MONONUCLEOTIDE, ... (6 entities in total)
• Functional Keywords: nitroreductase, haemophilus influenzae, 1-methyl-5-nitroimidazole, oxidoreductase
• Biological source: Haemophilus influenzae Rd KW20
• Total number of polymer chains: 2
• Total formula weight: 54719.06

Authors

Wanniarachchi, T.N.,Bruner, S.D. (deposition date: 2021-12-06, release date: 2022-02-23, Last modification date: 2023-10-18)

Primary citation

Liu, D.,Wanniarachchi, T.N.,Jiang, G.,Seabra, G.,Cao, S.,Bruner, S.D.,Ding, Y.
Biochemical and structural characterization of Haemophilus influenzae nitroreductase in metabolizing nitroimidazoles.
Rsc Chem Biol, 3:436-446, 2022

PubMed Abstract: Nitroheterocycle antibiotics, particularly 5-nitroimidazoles, are frequently used for treating anaerobic infections. The antimicrobial activities of these drugs heavily rely on the 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 (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 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.

PubMed: 35441146
DOI: 10.1039/d1cb00238d

Experimental method

X-RAY DIFFRACTION (2.2547 Å)