PDBsum entry 2e76

Photosynthesis

PDB id: 2e76

Contents

Protein chains

215 a.a. *

160 a.a. *

288 a.a. *

168 a.a. *

32 a.a. *

32 a.a. *

37 a.a. *

29 a.a. *

Ligands

HEM ×4

OPC ×2

UMQ ×4

CLA

TDS ×2

FES

SQD

BCR

Metals

_CD

Waters ×5

* Residue conservation analysis

PDB id:

2e76

Name:

Photosynthesis

Title:

Crystal structure of the cytochrome b6f complex with tridecyl- stigmatellin (tds) from m.Laminosus

Structure:

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

Source:

Mastigocladus laminosus. Organism_taxid: 83541. Organism_taxid: 83541

Resolution:

3.41Å R-factor: 0.188 R-free: 0.256

Authors:

W.A.Cramer,E.Yamashita,H.Zhang

Key ref:

E.Yamashita et al. (2007). Structure of the Cytochrome b(6)f Complex: Quinone Analogue Inhibitors as Ligands of Heme c(n). J Mol Biol, 370, 39-52. PubMed id: 17498743 DOI: 10.1016/j.jmb.2007.04.011

Date:

05-Jan-07 Release date: 12-Jun-07

Protein chain

P83791  (CYB6_MASLA) -  Cytochrome b6 from Mastigocladus laminosus

Seq: 215 a.a.

Struc: 215 a.a.

Protein chain

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

Seq: 160 a.a.

Struc: 160 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: 168 a.a.

Protein chain

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

Seq: 32 a.a.

Struc: 32 a.a.

Protein chain

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

Seq: 35 a.a.

Struc: 32 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: 29 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 = TDS) matches with 40.62% 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.jmb.2007.04.011

J Mol Biol 370:39-52 (2007)

PubMed id: 17498743

Structure of the Cytochrome b(6)f Complex: Quinone Analogue Inhibitors as Ligands of Heme c(n).

E.Yamashita, H.Zhang, W.A.Cramer.

ABSTRACT

A native structure of the cytochrome b(6)f complex with improved resolution was obtained from crystals of the complex grown in the presence of divalent cadmium. Two Cd(2+) binding sites with different occupancy were determined: (i) a higher affinity site, Cd1, which bridges His143 of cytochrome f and the acidic residue, Glu75, of cyt b(6); in addition, Cd1 is coordinated by 1-2 H(2)O or 1-2 Cl(-); (ii) a second site, Cd2, of lower affinity for which three identified ligands are Asp58 (subunit IV), Glu3 (PetG subunit) and Glu4 (PetM subunit). Binding sites of quinone analogue inhibitors were sought to map the pathway of transfer of the lipophilic quinone across the b(6)f complex and to define the function of the novel heme c(n). Two sites were found for the chromone ring of the tridecyl-stigmatellin (TDS) quinone analogue inhibitor, one near the p-side [2Fe-2S] cluster. A second TDS site was found on the n-side of the complex facing the quinone exchange cavity as an axial ligand of heme c(n). A similar binding site proximal to heme c(n) was found for the n-side inhibitor, NQNO. Binding of these inhibitors required their addition to the complex before lipid used to facilitate crystallization. The similar binding of NQNO and TDS as axial ligands to heme c(n) implies that this heme utilizes plastoquinone as a natural ligand, thus defining an electron transfer complex consisting of hemes b(n), c(n), and PQ, and the pathway of n-side reduction of the PQ pool. The NQNO binding site explains several effects associated with its inhibitory action: the negative shift in heme c(n) midpoint potential, the increased amplitude of light-induced heme b(n) reduction, and an altered EPR spectrum attributed to interaction between hemes c(n) and b(n). A decreased extent of heme c(n) reduction by reduced ferredoxin in the presence of NQNO allows observation of the heme c(n) Soret band in a chemical difference spectrum.

Selected figure(s)

Figure 1.
Figure 1. Two cadmium (Cd^2+) binding sites on the p-side of the M. laminosus b[6]f complex. (a) Position of higher occupancy site (Cd1) is close to the inter-monomer interface, and that of lower occupancy (Cd2) site is near the small subunits and the exterior of the complex. View is parallel to the plane of the membrane. Distances: (i) from Cd1 site, and (ii) from Cd2, to the [2Fe-2S] cluster on the same and opposite side monomer, (i) 38.9 Å and 40.1 Å, and (ii) 57.1 and 28.0 Å. Color code: cytochrome b[6] (cyan), subunit IV (purple), cytochrome f (red), ISP (yellow), PetG, PetL, PetM, and PetN (green). (b, stereo) Environment of Cd1 and Cd2 sites shown in more detail. Lower occupancy of the Cd2 site is shown by the smaller cage of electron density. A lipid molecule (possibly galactolipid) described in the coordinates of the C. reinhardtii b[6]f complex (pdb; 1Q90), but not previously discussed, is closer to Cd2. Distances: higher (Cd1) to lower occupancy (Cd2) Cd^2+ site, 23.2 Å; higher occupancy Cd1 site to heme b[p], 24.0 Å; Cd2 to residues Glu78, Trp79 and Y80 of the PEWY loop on the same monomer, 13, 12, and 16 Å. The seven peaks of largest amplitude in the anomalous difference map are: Cd1 site (18.5 σ), heme b[p] (18.1 σ), heme c[n] (17.6 σ), heme b[n] (17.0 σ), heme f (13.3 σ), [2Fe-2S] site (11.1 σ), Cd2 site (6.3 σ). The anomalous scattering factors (f letter double prime ) for Fe and Cd at 0.98 Å are 1.50 and 2.13, respectively. The B factors of the Cd1 and Cd2 sites are 80 Å^2 and 178 Å^2.

Figure 3.
Figure 3. F[o]–F[c] difference map of (a) p- and (b) n-side binding site of TDS in the b[6]f complex. (a) p-side. The extra density within H-bond distance of the His129 ligand of the [2Fe-2S] cluster and between the ef and cd1 loops is attributed to the chromone ring of TDS. As in Figure 2(a), the origin of the electron density under the cd2 loop, presumably lipid and/or detergent, is not known. (b) n-side. The position of TDS is shown relative to heme c[n], which is exposed to the quinone-exchange cavity. TDS is on the side of heme c[n] distal to heme b[n]. TM helices and surface helices within loops labeled as in Figure 2. F[o]–F[c] maps contoured at 4 σ.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 39-52) copyright 2007.

Figures were selected by the author.