PDBsum entry 2fyu

Oxidoreductase

PDB id: 2fyu

Contents

Protein chains

446 a.a. *

423 a.a. *

378 a.a. *

241 a.a. *

196 a.a. *

106 a.a. *

75 a.a. *

64 a.a. *

57 a.a. *

60 a.a. *

53 a.a. *

Ligands

HEM ×3

FDN

FES

Waters ×267

* Residue conservation analysis

PDB id:

2fyu

Name:

Oxidoreductase

Title:

Crystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor

Structure:

Ubiquinol-cytochromE-C reductase complex core protein i, mitochondrial. Chain: a. Fragment: core1. Ubiquinol-cytochromE-C reductase complex core protein 2, mitochondrial. Chain: b. Fragment: core2. Synonym: complex iii subunit ii.

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organism_taxid: 9913

Biol. unit:

22mer (from PDB file)

Resolution:

2.26Å R-factor: 0.249 R-free: 0.283

Authors:

D.Xia,L.Esser

Key ref:

L.Esser et al. (2006). Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1 complex. Proc Natl Acad Sci U S A, 103, 13045-13050. PubMed id: 16924113 DOI: 10.1073/pnas.0601149103

Date:

08-Feb-06 Release date: 29-Aug-06

Protein chain

P31800  (QCR1_BOVIN) -  Cytochrome b-c1 complex subunit 1, mitochondrial from Bos taurus

Seq: 480 a.a.

Struc: 446 a.a.

Protein chain

P23004  (QCR2_BOVIN) -  Cytochrome b-c1 complex subunit 2, mitochondrial from Bos taurus

Seq: 453 a.a.

Struc: 423 a.a.

Protein chain

P00157  (CYB_BOVIN) -  Cytochrome b from Bos taurus

Seq: 379 a.a.

Struc: 378 a.a.

Protein chain

P00125  (CY1_BOVIN) -  Cytochrome c1, heme protein, mitochondrial from Bos taurus

Seq: 325 a.a.

Struc: 241 a.a.

Protein chain

P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial from Bos taurus

Seq: 274 a.a.

Struc: 196 a.a.

Protein chain

P00129  (QCR7_BOVIN) -  Cytochrome b-c1 complex subunit 7 from Bos taurus

Seq: 111 a.a.

Struc: 106 a.a.*

Protein chain

P13271  (QCR8_BOVIN) -  Cytochrome b-c1 complex subunit 8 from Bos taurus

Seq: 82 a.a.

Struc: 75 a.a.

Protein chain

P00126  (QCR6_BOVIN) -  Cytochrome b-c1 complex subunit 6, mitochondrial from Bos taurus

Seq: 91 a.a.

Struc: 64 a.a.

Protein chain

P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial from Bos taurus

Seq: 274 a.a.

Struc: 57 a.a.

Protein chain

P00130  (QCR9_BOVIN) -  Cytochrome b-c1 complex subunit 9 from Bos taurus

Seq: 64 a.a.

Struc: 60 a.a.

Protein chain

P07552  (QCR10_BOVIN) -  Cytochrome b-c1 complex subunit 10 from Bos taurus

Seq: 56 a.a.

Struc: 53 a.a.

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

Enzyme reactions

• Enzyme class 2: Chains A, B, G, H, J, K: E.C.1.10.2.2 - Transferred entry: 7.1.1.8.
• Reaction: Quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H⁺
• Enzyme class 3: Chains D, E, I: E.C.7.1.1.8 - quinol--cytochrome-c reductase.
• Reaction: a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)- [cytochrome c](out) + 2 H(+)(out)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1073/pnas.0601149103

Proc Natl Acad Sci U S A 103:13045-13050 (2006)

PubMed id: 16924113

Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1 complex.

L.Esser, X.Gong, S.Yang, L.Yu, C.A.Yu, D.Xia.

ABSTRACT

In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation (Q(o)) site. The question remaining is how the motion of ISP is controlled so that only one electron enters the thermodynamically favorable chain via ISP. An analysis of eight structures of mitochondrial bc(1) with bound Q(o) site inhibitors revealed that the presence of inhibitors causes a bidirectional repositioning of the cd1 helix in the cytochrome b subunit. As the cd1 helix forms a major part of the ISP binding crater, any positional shift of this helix modulates the ability of cytochrome b to bind ISP. The analysis also suggests a mechanism for reversal of the ISP fixation when the shape complementarity is significantly reduced after a positional reorientation of the reaction product quinone. The importance of shape complementarity in this mechanism was confirmed by functional studies of bc(1) mutants and by a structure determination of the bacterial form of bc(1). A mechanism for the high fidelity of the bifurcated electron transfer is proposed.

Selected figure(s)

Figure 1.
Fig. 1. Prosthetic groups and subunit structures of the cyt bc[1] complex. (A) Arrangement of prosthetic groups in the dimeric bc[1] complex and illustration of the electron bifurcation at the Q[o] site. The b[L], b[H], and c[1] heme groups are shown as ball-and-stick models, and the [2Fe2S] clusters are depicted as cpk models. Carbon atoms, black; nitrogen, blue; oxygen, red; sulfur, yellow; iron, brown. The Q[o] pockets near the IMS side of the membrane and the Q[i] pockets near the matrix side are labeled and shaded in gray. Cyt c is shown as a gray shaded oval. Distances between redox centers are given on the left half of the diagram, and the redox potential for each center is given on the right. The high- and low-potential ET paths are depicted with red and green arrows, respectively. Circles in pink and light green within the Q[o] pockets are hypothesized distal-QH[2] and proximal-Q binding sites, respectively. (B) Ribbon diagram of the dimeric cyt b, cyt c[1], and ISP subunit in the mitochondrial bc[1] complex. Two symmetry-related cyt b subunits are shown (green and light green). The eight TM helices of cyt b are denoted with letters A–H. Helices A–E form one bundle in which the two b-type hemes (b[L] and b[H] in ball-and-stick models) reside; helices F–H form the other bundle. The ISP subunit (yellow and red for the symmetry pair) has an extrinsic soluble domain with a [2Fe2S] cluster at its tip, connecting to a TM segment by a flexible neck. The extrinsic domain of cyt c[1] (blue and magenta for the symmetry pair) with its heme group is rigidly attached to its TM helix. The locations for the two active sites (Q[o] and Q[i]) per monomer in cyt b are labeled. The surface depression in cyt b at the IMS side of the membrane is labeled as the ISP-docking crater.

Figure 3.
Fig. 3. Control of the ISP-ED motion switch and the proposed mechanism for electron bifurcation at the Q[o] pocket. The structural components necessary for the control of ISP conformational switch are illustrated in this cartoon rendition of the Q[o] pocket. The PEWY motif and cd1 helix in gray represent a native (Rest) configuration. The ISP in yellow and magenta are of oxidized and reduced form, respectively. The PEWY in blue stands for the open configuration with a bound Q[o] site inhibitor. The cd1 helix in red symbolizes the conformation (On/+) in the presence of a Pf inhibitor occupying the distal site (pink), and the cd1 helix in green shows the conformation (Off/–) when a Pm inhibitor is taking the proximal site (purple). Cyt c[1] and heme b[L] are also shown.

Figures were selected by an automated process.