2VR0

Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor

Summary for 2VR0

• Entry DOI: 10.2210/pdb2vr0/pdb
• Related: 2J7A
• Descriptor: CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA, NAPC/NIRT CYTOCHROME C FAMILY PROTEIN, HEME C, ... (6 entities in total)
• Functional Keywords: quinol dehydrogenase, oxidoreductase, hqno, nrfh, nrfha, membrane complex
• Biological source: DESULFOVIBRIO VULGARIS; More
• Total number of polymer chains: 6
• Total formula weight: 293098.73

Authors

Rodrigues, M.L.,Archer, M. (deposition date: 2008-03-24, release date: 2008-06-03, Last modification date: 2024-11-06)

Primary citation

Rodrigues, M.L.,Scott, K.A.,Sansom, M.S.P.,Pereira, I.A.C.,Archer, M.
Quinol Oxidation by C-Type Cytochromes: Structural Characterization of the Menaquinol Binding Site of Nrfha.
J.Mol.Biol., 381:341-, 2008

PubMed Abstract: Membrane-bound cytochrome c quinol dehydrogenases play a crucial role in bacterial respiration by oxidizing menaquinol and transferring electrons to various periplasmic oxidoreductases. In this work, the menaquinol oxidation site of NrfH was characterized by the determination of the X-ray structure of Desulfovibrio vulgaris NrfHA nitrite reductase complex bound to 2-heptyl-4-hydroxyquinoline-N-oxide, which is shown to act as a competitive inhibitor of NrfH quinol oxidation activity. The structure, at 2.8-A resolution, reveals that the inhibitor binds close to NrfH heme 1, where it establishes polar contacts with two essential residues: Asp89, the residue occupying the heme distal ligand position, and Lys82, a strictly conserved residue. The menaquinol binding cavity is largely polar and has a wide opening to the protein surface. Coarse-grained molecular dynamics simulations suggest that the quinol binding site of NrfH and several other respiratory enzymes lie in the head group region of the membrane, which probably facilitates proton transfer to the periplasm. Although NrfH is not a multi-span membrane protein, its quinol binding site has several characteristics similar to those of quinone binding sites previously described. The data presented here provide the first characterization of the quinol binding site of the cytochrome c quinol dehydrogenase family.

PubMed: 18597779
DOI: 10.1016/J.JMB.2008.05.066

Experimental method

X-RAY DIFFRACTION (2.8 Å)