PDBsum entry 4pv1

Electron transport/inhibitor

PDB id: 4pv1

Contents

Protein chains

213 a.a.

159 a.a.

288 a.a.

158 a.a.

28 a.a.

31 a.a.

37 a.a.

28 a.a.

Ligands

MYS

HEC ×4

UMQ ×3

SMA

7PH

8K6

CLA

OPC ×3

FES

SQD

BCR

Metals

_CD ×2

Waters ×16

PDB id:

4pv1

Name:

Electron transport/inhibitor

Title:

Cytochrome b6f structure from m. Laminosus with the quinone analog inhibitor stigmatellin

Structure:

Cytochrome b6. Chain: a. Cytochrome b6-f complex subunit 4. Chain: b. Synonym: 17 kda polypeptide. Apocytochrome f. Chain: c. Fragment: unp residues 45-333. Cytochrome b6-f complex iron-sulfur subunit.

Source:

Mastigocladus laminosus. Organism_taxid: 83541. Organism_taxid: 83541

Resolution:

3.00Å R-factor: 0.217 R-free: 0.247

Authors:

S.S.Hasan,E.Yamashita,W.A.Cramer

Key ref:

S.S.Hasan et al. (2014). Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal. Biophys J, 107, 1620-1628. PubMed id: 25296314 DOI: 10.1016/j.bpj.2014.08.003

Date:

14-Mar-14 Release date: 20-Aug-14

Protein chain

P83791  (CYB6_MASLA) -  Cytochrome b6 from Mastigocladus laminosus

Seq: 215 a.a.

Struc: 213 a.a.

Protein chain

P83792  (PETD_MASLA) -  Cytochrome b6-f complex subunit 4 from Mastigocladus laminosus

Seq: 160 a.a.

Struc: 159 a.a.

Protein chain

P83793  (CYF_MASLA) -  Cytochrome f from Mastigocladus laminosus

Seq: 333 a.a.

Struc: 288 a.a.*

Protein chain

P83794  (UCRI_MASLA) -  Cytochrome b6-f complex iron-sulfur subunit from Mastigocladus laminosus

Seq: 179 a.a.

Struc: 158 a.a.

Protein chain

P83795  (PETL_MASLA) -  Cytochrome b6-f complex subunit 6 from Mastigocladus laminosus

Seq: 32 a.a.

Struc: 28 a.a.

Protein chain

P83796  (PETM_MASLA) -  Cytochrome b6-f complex subunit 7 from Mastigocladus laminosus

Seq: 35 a.a.

Struc: 31 a.a.

Protein chain

P83797  (PETG_MASLA) -  Cytochrome b6-f complex subunit 5 from Mastigocladus laminosus

Seq: 37 a.a.

Struc: 37 a.a.

Protein chain

P83798  (PETN_MASLA) -  Cytochrome b6-f complex subunit 8 from Mastigocladus laminosus

Seq: 29 a.a.

Struc: 28 a.a.

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

Enzyme reactions

• Enzyme class: Chain D: E.C.7.1.1.6 - plastoquinol--plastocyanin reductase.
• Reaction: 2 oxidized [plastocyanin] + a plastoquinol + 2 H⁺(in) = 2 reduced [plastocyanin] + a plastoquinone + 4 H⁺(out)

2 × oxidized [plastocyanin] (Bound ligand (Het Group name = MYS) matches with 50.00% similarity) + plastoquinol + 2 × H(+)(in) = 2 × reduced [plastocyanin] + plastoquinone + 4 × H(+)(out)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.bpj.2014.08.003

Biophys J 107:1620-1628 (2014)

PubMed id: 25296314

Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal.

S.S.Hasan, E.A.Proctor, E.Yamashita, N.V.Dokholyan, W.A.Cramer.

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 Å 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.