PDBsum entry: 1kyo

Oxidoreductase/electron transport

PDB-id: 1kyo

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

430 a.a. *

352 a.a. *

385 a.a. *

245 a.a. *

185 a.a. *

74 a.a. *

125 a.a. *

93 a.a. *

53 a.a. *

127 a.a. *

107 a.a. *

108 a.a. *

Ligands

HEM ×7

FES ×2

SMA ×2

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1kyo

Name:

Oxidoreductase/electron transport

Title:

Yeast cytochrome bc1 complex with bound substrate cytochromE C

Structure:

Ubiquinol-cytochromE C reductase complex core protein i. Chain: a, l. Fragment: residues 27-457. Ubiquinol-cytochromE C reductase complex core protein 2. Chain: b, m. Fragment: residues 17-368. Cytochrome b.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organelle: mitochondria. Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

23mer (from PQS)

UniProt:

Chains A, L: P07256 (QCR1_YEAST)

Seq:
Struc:
	Seq:	457 a.a.
	Struc:	430 a.a.*

Chains B, M: P07257 (QCR2_YEAST)

Seq:
Struc:
	Seq:	368 a.a.
	Struc:	352 a.a.

Chains C, N: P00163 (CYB_YEAST)

Seq:
Struc:
	Seq:	385 a.a.
	Struc:	385 a.a.*

Chains D, O: P07143 (CY1_YEAST)

Seq:
Struc:
	Seq:	309 a.a.
	Struc:	245 a.a.

Chains E, P: P08067 (UCRI_YEAST)

Seq:	215 a.a.
Struc:	185 a.a.

Chains F, Q: P00127 (QCR6_YEAST)

Seq:	147 a.a.
Struc:	74 a.a.*

Chains G, R: P00128 (QCR7_YEAST)

Seq:	127 a.a.
Struc:	125 a.a.

Chains H, S: P08525 (QCR8_YEAST)

Seq:	94 a.a.
Struc:	93 a.a.

Chains I, T: P22289 (QCR9_YEAST)

Seq:	66 a.a.
Struc:	53 a.a.*

Chain W: P00044 (CYC1_YEAST)

Seq:

109 a.a.

Struc:

108 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme class:

Chains E, P: E.C.1.10.2.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

QH₂ + 2 ferricytochrome c = Q + 2 ferrocytochrome c + 2 H⁺ (see diagram below)

Resolution:

2.97Å

R-factor:

0.229

R-free:

0.268

Authors:

C.Lange,C.Hunte

Key ref:

C.Lange and C.Hunte (2002). Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c.. Proc Natl Acad Sci U S A, 99, 2800-2805. [PubMed id: 11880631] [DOI: 10.1073/pnas.052704699]

Date:

05-Feb-02

Release date:

06-Mar-02

Related entries:

1ezv
yeast cytochrome bc1 complex crystallized with an antibody
fv fragment
1kb9
phospholipid-binding in the yeast cytochrome bc1 complex
rystallized with an antibody fv fragment

Quick_links

Procheck

Key reference

DOI no: 10.1073/pnas.052704699

Proc Natl Acad Sci U S A 99:2800-2805 (2002)

PubMed id: 11880631

Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c.

C.Lange, C.Hunte.

ABSTRACT

Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to integral membrane proteins. Specific and transient complexes need to be formed between the redox partners to ensure fast turnover. In respiration, the mobile electron carrier cytochrome c shuttles electrons from the cytochrome bc1 complex to cytochrome c oxidase. Despite extensive studies of this fundamental step of energy metabolism, the structures of the respective electron transfer complexes were not known. Here we present the crystal structure of the complex between cytochrome c and the cytochrome bc1 complex from Saccharomyces cerevisiae. The complex was crystallized with the help of an antibody fragment, and its structure was determined at 2.97-A resolution. Cytochrome c is bound to subunit cytochrome c1 of the enzyme. The tight and specific interactions critical for electron transfer are mediated mainly by nonpolar forces. The close spatial arrangement of the c-type hemes unexpectedly suggests a direct and rapid heme-to-heme electron transfer at a calculated rate of up to 8.3 x 10(6) s(-1). Remarkably, cytochrome c binds to only one recognition site of the homodimeric multisubunit complex. Interestingly, the occupancy of quinone in the Qi site is higher in the monomer with bound cytochrome c, suggesting a coordinated binding and reduction of both electron-accepting substrates. Obviously, cytochrome c reduction by the cytochrome bc1 complex can be regulated in response to respiratory conditions.

Selected figure(s)

Figure 1.
Fig. 1. (A) Half-of-the-sites binding of CYC to the homodimeric QCR. The overall structure of the complex between the redox partners CYC and QCR with bound Fv fragment is shown. Protein subunits are depicted in ribbon representation with respective colors: CYC (yellow), CYT1 (red), cytochrome b (blue), RIP1 (green), QCR6 (cyan), and Fv fragment (orange). All other subunits are colored in gray. Redox cofactors (ball-and-stick representation) are colored in black. The complex is viewed parallel to the plane of the inner membrane (IM) that separates the intermembrane space (IMS) from the matrix (MA). The position of the inner membrane is indicated as gray boxes. (B) Close-up view of the recognition site (indicated by a black frame in A) showing the experimental electron-density map before inclusion of CYC to the model. The 2F[obs] F[calc] electron-density map (blue) is contoured at 1 , and the corresponding part of the refined model (ball-and-stick presentation) is superimposed. The orientations of the CYC polypeptide (yellow) and its cofactor heme c (green) are unambiguously defined by distinct electron density. Protein residues of CYT1 and heme c[1] are colored in red and magenta, respectively. The figure was generated by using the programs MOLSCRIPT (36) and BOBSCRIPT (37).

Figure 2.
Fig. 2. The complementary recognition sites in the QCR/CYC complex. Surface representations of CYC and CYT1 are shown on Left and Right, respectively. (A) Residues that are involved in CYC binding and have intermolecular contacts of less than 4 Å are colored in green. (B) Residues, which are hydrophobic, are colored in orange. (C) Side chains, which have positive or negative full charges, are colored in blue or red, respectively. Color maxima correspond to +25 and 25 k[B]T. The figure was generated by using GRASP (38).

Figures were selected by the author.