PDBsum entry 1w3r

Antibiotic resistance

PDB id: 1w3r

Contents

Protein chain

204 a.a. *

Ligands

ACT

PYR

2MN

Waters ×293

* Residue conservation analysis

PDB id:

1w3r

Name:

Antibiotic resistance

Title:

Nima from d. Radiodurans with metronidazole and pyruvate

Structure:

Nima-related protein. Chain: a. Synonym: 5-nitroimidazole antibiotic resistance protein. Engineered: yes

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.90Å R-factor: 0.192 R-free: 0.256

Authors:

H.-K.S.Leiros,S.Kozielski-Stuhrmann,U.Kapp,L.Terradot,G.A.Leonard, S.M.Mcsweeney

Key ref:

H.K.Leiros et al. (2004). Structural basis of 5-nitroimidazole antibiotic resistance: the crystal structure of NimA from Deinococcus radiodurans. J Biol Chem, 279, 55840-55849. PubMed id: 15492014 DOI: 10.1074/jbc.M408044200

Date:

17-Jul-04 Release date: 18-Oct-04

Protein chain

Q9RW27  (Q9RW27_DEIRA) -  NimA-related protein from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 195 a.a.

Struc: 204 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.M408044200

J Biol Chem 279:55840-55849 (2004)

PubMed id: 15492014

Structural basis of 5-nitroimidazole antibiotic resistance: the crystal structure of NimA from Deinococcus radiodurans.

H.K.Leiros, S.Kozielski-Stuhrmann, U.Kapp, L.Terradot, G.A.Leonard, S.M.McSweeney.

ABSTRACT

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.

Selected figure(s)

Figure 5.
FIG. 5. a, Fourier difference map (F[o] - F[c]) at 3 with the pyruvate residue omitted from the refinement of the native drNimA structure. The finally refined pyruvate is given along with some surrounding residues. b, a LIGPLOT (41) presentation of the chemical environments of the pyruvate in the final drNimA structure, with inter-atomic distances for polar interactions.

Figure 7.
FIG. 7. Proposed antibiotic resistance mechanism. Step , this is from the native drNimA structure to the covalently bound pyruvate structure (drNimA-Pyr), an oxidation of His-71 and pyruvate into a His-71-Pyr residue, a reaction that releases 2e^- and H+. Step , the released electrons can further be used to reduce the antibiotic. Because the antibiotic gets 2e^-, it prevents formation of the toxic bactericidal radical as given in Fig. 1. Our drNimA-MTR structure seems to be an intermediate, which is located somewhere along Step in between the native drNimA and the drNimA-Pyr complex.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 55840-55849) copyright 2004.

Figures were selected by an automated process.