PDBsum entry 2ibz

Oxidoreductase

PDB id: 2ibz

Contents

Protein chains

431 a.a. *

352 a.a. *

385 a.a. *

245 a.a. *

185 a.a. *

74 a.a. *

125 a.a. *

93 a.a. *

55 a.a. *

127 a.a. *

107 a.a. *

Ligands

HEC ×3

UQ6

SMA

FES

Waters ×340

* Residue conservation analysis

PDB id:

2ibz

Name:

Oxidoreductase

Title:

Yeast cytochrome bc1 complex with stigmatellin

Structure:

Ubiquinol-cytochromE-C reductase complex core protein 1. Chain: a. Synonym: complex iii subunit 1, cytochrome b-c1 complex subunit 1. Ubiquinol-cytochromE-C reductase complex core protein 2. Chain: b. Synonym: complex iii subunit 2, cytochrome b-c1 complex subunit 2, ubiquinol:cytochromE-C oxidoreductase subunit ii. Cytochrome b. Chain: c.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Mus musculus. House mouse. Organism_taxid: 10090. Gene: variable domain antibody heavy chain. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.222 R-free: 0.256

Authors:

C.Hunte

Key ref:

C.R.Lancaster et al. (2007). A comparison of stigmatellin conformations, free and bound to the photosynthetic reaction center and the cytochrome bc1 complex. J Mol Biol, 368, 197-208. PubMed id: 17337272 DOI: 10.1016/j.jmb.2007.02.013

Date:

12-Sep-06 Release date: 20-Mar-07

Protein chain

P07256  (QCR1_YEAST) -  Cytochrome b-c1 complex subunit 1, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 457 a.a.

Struc: 431 a.a.*

Protein chain

P07257  (QCR2_YEAST) -  Cytochrome b-c1 complex subunit 2, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 368 a.a.

Struc: 352 a.a.

Protein chain

P00163  (CYB_YEAST) -  Cytochrome b from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 385 a.a.

Struc: 385 a.a.*

Protein chain

P07143  (CY1_YEAST) -  Cytochrome c1, heme protein, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 309 a.a.

Struc: 245 a.a.

Protein chain

P08067  (UCRI_YEAST) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 185 a.a.

Protein chain

P00127  (QCR6_YEAST) -  Cytochrome b-c1 complex subunit 6, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 147 a.a.

Struc: 74 a.a.

Protein chain

P00128  (QCR7_YEAST) -  Cytochrome b-c1 complex subunit 7, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 127 a.a.

Struc: 125 a.a.

Protein chain

P08525  (QCR8_YEAST) -  Cytochrome b-c1 complex subunit 8, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 94 a.a.

Struc: 93 a.a.

Protein chain

P22289  (QCR9_YEAST) -  Cytochrome b-c1 complex subunit 9, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 66 a.a.

Struc: 55 a.a.

Protein chain

P18531  (HVM60_MOUSE) -  Ig heavy chain V region 3-6 from Mus musculus

Seq: 116 a.a.

Struc: 127 a.a.*

Protein chain

A0N6Y3  (A0N6Y3_9MURI) -  F30C7 light chain variable region (Fragment) from Mus sp

Seq: 107 a.a.

Struc: 107 a.a.*

* PDB and UniProt seqs differ at 31 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B, H, F, G, I: 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 C, D, E: 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: 10.1016/j.jmb.2007.02.013

J Mol Biol 368:197-208 (2007)

PubMed id: 17337272

A comparison of stigmatellin conformations, free and bound to the photosynthetic reaction center and the cytochrome bc1 complex.

C.R.Lancaster, C.Hunte, J.Kelley, B.L.Trumpower, R.Ditchfield.

ABSTRACT

We describe in detail the conformations of the inhibitor stigmatellin in its free form and bound to the ubiquinone-reducing (Q(B)) site of the reaction center and to the ubiquinol-oxidizing (Q(o)) site of the cytochrome bc(1) complex. We present here the first structures of a stereochemically correct stigmatellin in complexes with a bacterial reaction center and the yeast cytochrome bc1 complex. The conformations of the inhibitor bound to the two enzymes are not the same. We focus on the orientations of the stigmatellin side-chain relative to the chromone head group, and on the interaction of the stigmatellin side-chain with these membrane protein complexes. The different conformations of stigmatellin found illustrate the structural variability of the Q sites, which are affected by the same inhibitor. The free rotation about the chi1 dihedral angle is an essential factor for allowing stigmatellin to bind in both the reaction center and the cytochrome bc1 pocket.

Selected figure(s)

Figure 5.
Figure 5. A comparison of non-bonding interactions at the stigmatellin-binding sites of (a) the Rp. viridis RC and (b) the S. cerevisiae cytochrome bc[1] complex. For clarity, interactions involving the chromone head group other than hydrogen bonding interactions (shown in light blue)^13.^ and ^14. are omitted. Labelled cyt bc[1] complex residues are from cytochrome b with the exception of the Rieske protein residue His181*. Interatomic distances of equal to or less than 4.0 Å involving the first half of the stigmatellin tail are indicated in red, those with the second, terminal half, in green. For clarity, in cases of multiple interactions fulfilling the distance criterion for the same stigmatellin atom, only the shortest distances are shown.

Figure 6.
Figure 6. Preference in the RC Q[B] site for the distorted stigmatellin conformer (Stereo view). RC residues that prevent the binding of stigmatellin in the theoretical lowest energy type 1 conformation (light blue) and in the cyt bc[1]-bound type 2 conformation (pink). Otherwise, color-coding and labeling are the same as in Figure 4.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 368, 197-208) copyright 2007.

Figures were selected by an automated process.