7N9Z

E. coli cytochrome bo3 in MSP nanodisc

Summary for 7N9Z

• Entry DOI: 10.2210/pdb7n9z/pdb
• EMDB information: 24265 30471 30474 30475 30817 30818 30819
• Descriptor: Cytochrome o ubiquinol oxidase, subunit I, CARDIOLIPIN, COPPER (II) ION, ... (13 entities in total)
• Functional Keywords: ubiquinone, heme-copper oxidoreductase, electron transport, bioenergetics, proton pump, membrane protein
• Biological source: Escherichia coli; More
• Total number of polymer chains: 4
• Total formula weight: 155829.95

Authors

Vallese, F.,Clarke, O.B. (deposition date: 2021-06-19, release date: 2021-09-01, Last modification date: 2024-06-05)

Primary citation

Li, J.,Han, L.,Vallese, F.,Ding, Z.,Choi, S.K.,Hong, S.,Luo, Y.,Liu, B.,Chan, C.K.,Tajkhorshid, E.,Zhu, J.,Clarke, O.,Zhang, K.,Gennis, R.
Cryo-EM structures of Escherichia coli cytochrome bo 3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme , heme , and Cu), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75 and R71 In both structures, residue H98 occupies two conformations. In conformation 1, H98 forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 has flipped to form a hydrogen bond with E14 at the N-terminal end of TM0. We propose that H98 dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98.

PubMed: 34417297
DOI: 10.1073/pnas.2106750118

Experimental method

ELECTRON MICROSCOPY (2.19 Å)