4PV1: Cytochrome B6f Structure From M. Laminosus With The Quinone Analog Inhibitor Stigmatellin

Citation:
Abstract
The cytochrome bc complexes b6f and bc1 catalyze proton-coupled quinol/quinone redox reactions to generate a transmembrane proton electrochemical gradient. Quinol oxidation on the electrochemically positive (p) interface of the complex occurs at the end of a narrow quinol/quinone entry/exit Qp portal, 11 A long in bc complexes. Superoxide, which has multiple signaling functions, is a by-product of the p-side quinol oxidation. Although the transmembrane core and the chemistry of quinone redox reactions are conserved in bc complexes, the rate of superoxide generation is an order of magnitude greater in the b6f complex, implying that functionally significant differences in structure exist between the b6f and bc1 complexes on the p-side. A unique structure feature of the b6f p-side quinol oxidation site is the presence of a single chlorophyll-a molecule whose function is unrelated to light harvesting. This study describes a cocrystal structure of the cytochrome b6f complex with the quinol analog stigmatellin, which partitions in the Qp portal of the bc1 complex, but not effectively in b6f. It is inferred that the Qp portal is partially occluded in the b6f complex relative to bc1. Based on a discrete molecular-dynamics analysis, occlusion of the Qp portal is attributed to the presence of the chlorophyll phytyl tail, which increases the quinone residence time within the Qp portal and is inferred to be a cause of enhanced superoxide production. This study attributes a novel (to our knowledge), structure-linked function to the otherwise enigmatic chlorophyll-a in the b6f complex, which may also be relevant to intracellular redox signaling.
PDB ID: 4PV1Download
MMDB ID: 122560
PDB Deposition Date: 2014/3/14
Updated in MMDB: 2014/08
Experimental Method:
x-ray diffraction
Resolution: 3  Å
Source Organism:
Similar Structures:
Biological Unit for 4PV1: hexadecameric; determined by author and by software (PISA)
Molecular Components in 4PV1
Label Count Molecule
Proteins (16 molecules)
2
Cytochrome B6
Molecule annotation
2
Cytochrome B6-f Complex Subunit 4
Molecule annotation
2
Apocytochrome F
Molecule annotation
2
Cytochrome B6-f Complex Iron-sulfur Subunit
Molecule annotation
2
Cytochrome B6-f Complex Subunit 6
Molecule annotation
2
Cytochrome B6-f Complex Subunit 7
Molecule annotation
2
Cytochrome B6-f Complex Subunit 5
Molecule annotation
2
Cytochrome B6-f Complex Subunit 8
Molecule annotation
Chemicals (40 molecules)
1
2
2
4
3
8
4
6
5
2
6
2
7
2
8
2
9
6
10
2
11
2
12
2
* Click molecule labels to explore molecular sequence information.

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