PDBsum entry 2d2c

Photosynthesis

PDB id: 2d2c

Contents

Protein chains

202 a.a. *

137 a.a. *

286 a.a. *

168 a.a. *

32 a.a. *

35 a.a. *

27 a.a. *

27 a.a. *

Ligands

HEM ×6

HEC ×2

OPC ×4

BNT ×2

CLA ×2

FES ×2

BCR ×2

Waters ×2

* Residue conservation analysis

PDB id:

2d2c

Name:

Photosynthesis

Title:

Crystal structure of cytochrome b6f complex with dbmib from m. Laminosus

Structure:

Cytochrome b6. Chain: a, n. Cytochrome b6-f complex subunit 4. Chain: b, o. Synonym: 17 kda polypeptide. Apocytochrome f. Chain: c, p. Cytochrome b6-f complex iron-sulfur subunit. Chain: d, q.

Source:

Mastigocladus laminosus. Organism_taxid: 83541. Organism_taxid: 83541

Biol. unit:

60mer (from PQS)

Resolution:

3.80Å R-factor: 0.276 R-free: 0.378

Authors:

J.Yan,G.Kurisu,W.A.Cramer

Key ref:

J.Yan et al. (2006). Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex. Proc Natl Acad Sci U S A, 103, 69-74. PubMed id: 16371475

Date:

07-Sep-05 Release date: 13-Dec-05

Protein chains

P83791  (CYB6_MASLA) -  Cytochrome b6 from Mastigocladus laminosus

Seq: 215 a.a.

Struc: 202 a.a.

Protein chains

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

Seq: 160 a.a.

Struc: 137 a.a.*

Protein chains

P83793  (CYF_MASLA) -  Cytochrome f from Mastigocladus laminosus

Seq: 333 a.a.

Struc: 286 a.a.*

Protein chains

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

Seq: 179 a.a.

Struc: 168 a.a.*

Protein chains

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

Seq: 32 a.a.

Struc: 32 a.a.

Protein chains

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

Seq: 35 a.a.

Struc: 35 a.a.

Protein chains

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

Seq: 37 a.a.

Struc: 27 a.a.

Protein chains

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

Seq: 29 a.a.

Struc: 27 a.a.

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains D, Q: 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 = BNT) matches with 61.11% 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

Proc Natl Acad Sci U S A 103:69-74 (2006)

PubMed id: 16371475

Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex.

J.Yan, G.Kurisu, W.A.Cramer.

ABSTRACT

Details are presented of the structural analysis of the cytochrome b(6)f complex from the thermophilic cyanobacterium, Mastigocladus laminosus, in the presence of the electrochemically positive (p)-side quinone analogue inhibitor, 2,5-dibromo-3-methyl-6-isopropylbenzoquinone (DBMIB). One DBMIB binding site was found. This site is peripheral to the quinone binding space defined by the binding sites of other p-side inhibitors previously resolved in cytochrome bc(1)/b(6)f complexes. This high-affinity site resides in a p-side interfacial niche bounded by cytochrome f, subunit IV, and cytochrome b(6), is close (8 A) to the p-side heme b, but distant (19 A) from the [2Fe-2S] cluster. No significant electron density associated with the DBMIB was found elsewhere in the structure. However, the site at which DBMIB can inhibit light-induced redox turnover is within a few A of the [2Fe-2S] cluster, as shown by the absence of inhibition in mutants of Synechococcus sp. PCC 7002 at iron sulfur protein-Leu-111 near the cluster. The ability of a minimum amount of initially oxidized DBMIB to inhibit turnover of WT complex after a second light flash implies that there is a light-activated movement of DBMIB from the distal peripheral site to an inhibitory site proximal to the [2Fe-2S] cluster. Together with the necessary passage of quinone/quinol through the small Q(p) portal in the complex, it is seen that transmembrane traffic of quinone-like molecules through the core of cytochrome bc complexes can be labyrinthine.