Structural basis of 5-nitroimidazole antibiotic resistance: the crystal structure of NimA from Deinococcus radiodurans.
5-Nitroimidazole-based antibiotics are compounds extensively used for treating infections in humans and animals caused by several important pathogens. They are administered as prodrugs, and their activation depends upon an anaerobic 1-electron reduction of the nitro group by a reduction pathway in the cells. Bacterial resistance toward these drugs is thought to be caused by decreased drug uptake and/or an altered reduction efficiency. One class of resistant strains, identified in Bacteroides, has been shown to carry Nim genes (NimA, -B, -C, -D, and -E), which encode for reductases that convert the nitro group on the antibiotic into a non-bactericidal amine. In this paper, we have described the crystal structure of NimA from Deinococcus radiodurans (drNimA) at 1.6 A resolution. We have shown that drNimA is a homodimer in which each monomer adopts a beta-barrel fold. We have identified the catalytically important His-71 along with the cofactor pyruvate and antibiotic binding sites, all of which are found at the monomer-monomer interface. We have reported three additional crystal structures of drNimA, one in which the antibiotic metronidazole is bound to the protein, one with pyruvate covalently bound to His-71, and one with lactate covalently bound to His-71. Based on these structures, a reaction mechanism has been proposed in which the 2-electron reduction of the antibiotic prevents accumulation of the toxic nitro radical. This mechanism suggests that Nim proteins form a new class of reductases, conferring resistance against 5-nitroimidazole-based antibiotics.
Leiros
Hanna-Kirsti S
HK
Macromolecular Crystallography Group, European Synchrotron Radiation Facility, BP 220, 6 Rue Jules Horowitz, F-38043 Grenoble Cedex 09, France.
Kozielski-Stuhrmann
Sigrid
S
Kapp
Ulrike
U
Terradot
Laurent
L
Leonard
Gordon A
GA
McSweeney
Seán M
SM
D000900:Anti-Bacterial Agents / Q000737:chemistry; D000890:Anti-Infective Agents / Q000494:pharmacology; D001665:Binding Sites; D002850:Chromatography, Gel; D018360:Crystallography, X-Ray; D034301:Deinococcus / Q000378:metabolism*; D019281:Dimerization; D024881:Drug Resistance, Bacterial; D004583:Electrons; D004591:Electrophoresis, Polyacrylamide Gel; D005583:Fourier Analysis; D006639:Histidine / Q000737:chemistry; D008795:Metronidazole / Q000494:pharmacology; D008956:Models, Chemical; D008958:Models, Molecular; D009593:Nitroimidazoles / Q000737:chemistry / Q000494:pharmacology*; D009601:Nitroreductases / Q000096:biosynthesis* / Q000737:chemistry*
D000900:Anti-Bacterial Agents; D000890:Anti-Infective Agents; D009593:Nitroimidazoles; D008795:Metronidazole; D006639:Histidine; D009601:Nitroreductases; C052587:4-nitroimidazole