PDBsum entry: 1kb9

Oxidoreductase/electron transport

PDB-id: 1kb9

Asymmetric unit

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Description

Header details

Header records

References

PROCHECK

Protein chains

431 a.a. *

352 a.a. *

385 a.a. *

246 a.a. *

185 a.a. *

74 a.a. *

125 a.a. *

93 a.a. *

55 a.a. *

127 a.a. *

107 a.a. *

Ligands

PCF

UMQ

HEM ×3

SMA

UQ6

PIE

PEF ×2

CDL

FES

Waters ×321

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, 22mer
(*as deduced by PQS)

PDB id:

1kb9

Name:

Oxidoreductase/electron transport

Title:

Yeast cytochrome bc1 complex

Structure:

Ubiquinol-cytochromE C reductase complex core protein i. Chain: a. Fragment: residues 27-457. Engineered: yes. Ubiquinol-cytochromE C reductase complex core protein 2. Chain: b. Fragment: residues 17-368.

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:

22mer (from PQS)

UniProt:

Chain A: P07256 (QCR1_YEAST)

Seq:
Struc:
	Seq:	457 a.a.
	Struc:	431 a.a.*

Chain B: P07257 (QCR2_YEAST)

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

Chain C: P00163 (CYB_YEAST)

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

Chain D: P07143 (CY1_YEAST)

Seq:
Struc:
	Seq:	309 a.a.
	Struc:	246 a.a.

Chain E: P08067 (UCRI_YEAST)

Seq:	215 a.a.
Struc:	185 a.a.

Chain F: P00127 (QCR6_YEAST)

Seq:	147 a.a.
Struc:	74 a.a.

Chain G: P00128 (QCR7_YEAST)

Seq:	127 a.a.
Struc:	125 a.a.

Chain H: P08525 (QCR8_YEAST)

Seq:	94 a.a.
Struc:	93 a.a.

Chain I: P22289 (QCR9_YEAST)

Seq:

66 a.a.

Struc:

55 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme class:

Chain E: 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:

2.30Å

R-factor:

0.218

R-free:

0.249

Authors:

C.Lange,J.H.Nett,B.L.Trumpower,C.Hunte

Key ref:

C.Lange et al. (2001). Specific roles of protein-phospholipid interactions in the yeast cytochrome bc1 complex structure.. EMBO J, 20, 6591-6600. [PubMed id: 11726495] [DOI: 10.1093/emboj/20.23.6591]

Date:

05-Nov-01

Release date:

18-Sep-02

Related entries:

1ezv
structure of the yeast cytochrome bc1 complex co-
crystallized with an antibody fv-fragment

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Key reference

DOI no: 10.1093/emboj/20.23.6591

EMBO J 20:6591-6600 (2001)

PubMed id: 11726495

Specific roles of protein-phospholipid interactions in the yeast cytochrome bc1 complex structure.

C.Lange, J.H.Nett, B.L.Trumpower, C.Hunte.

ABSTRACT

Biochemical data have shown that specific, tightly bound phospholipids are essential for activity of the cytochrome bc1 complex (QCR), an integral membrane protein of the respiratory chain. However, the structure and function of such phospholipids are not yet known. Here we describe five phospholipid molecules and one detergent molecule in the X-ray structure of yeast QCR at 2.3 A resolution. Their individual binding sites suggest specific roles in facilitating structural and functional integrity of the enzyme. Interestingly, a phosphatidylinositol molecule is bound in an unusual interhelical position near the flexible linker region of the Rieske iron-sulfur protein. Two possible proton uptake pathways at the ubiquinone reduction site have been identified: the E/R and the CL/K pathway. Remarkably, cardiolipin is positioned at the entrance to the latter. We propose that cardiolipin ensures structural integrity of the proton-conducting protein environment and takes part directly in proton uptake. Site-directed mutagenesis of ligating residues confirmed the importance of the phosphatidylinositol- and cardiolipin-binding sites.

Selected figure(s)

Figure 5.
Figure 5 Section of the yeast QCR model showing L5 (cardiolipin), neighboring amino acid residues and water molecules. Hydrogen bonds or ion pairs with the oxygen atoms of the phosphodiester groups A and B of the cardiolipin headgroup are indicated as dashed lines (Lys288, Lys289 of CYT1, Tyr28 of COB). Water molecules are shown as balls, and other molecules in stick presentation. The final 2F[o] - F[c] electron density map (blue -gray) is contoured at 1.0 . Atoms are shown in standard colors.

Figure 7.
Figure 7 Putative proton uptake pathways at the Q[i] site of yeast QCR via two arrays of hydrogen-bonded water molecules, which connect the bulk solvent at the matrix side with the site of ubiquinone reduction. The entrance to the E/R pathway is formed by Glu52 of QCR7 and Wat176. The gating residue towards the quinone-binding pocket is Arg218 of COB. Cardiolipin (L5) is positioned at the entrance to the CL/K pathway, for which Lys228 of COB is the gating residue. Arrows indicate the access sites from the bulk solvent, and double arrows show proton transfer between the key residues Arg218 or Lys228 of COB and UQ6. Side chains of amino acid residues that are involved in hydrogen bond interactions or ion pair formation are shown (standard colors). Dashed lines indicate hydrogen bond interactions. Dotted lines are used for hydrogen bond interactions of UQ6 and CL ligands (His202, Asp229 and Tyr28 of COB, and Lys288 and Lys289 of CYT1). Water molecules in the cavity above the cardiolipin headgroup are stabilized by interactions with side chains of Lys228 of COB, Lys296 of CYT1 and His85 of QCR7. A surrounding layer of non-polar residues (not shown) encloses the water-filled cavity. Transmembrane helices are shown as ribbon presentation and other polypeptide backbones as rope presentation. UQ6, heme b[H] and CL are represented as stick models.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 6591-6600) copyright 2001.

Figures were selected by the author.