PDBsum entry: 1p84

Oxidoreductase

PDB-id: 1p84

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

3PH ×2

UMQ

HEM ×3

DBT

UQ6

3PE ×2

PC1

CDL

FES

Waters ×326

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, 22mer
- as defined in PDB file (see also PQS)

PDB id:

1p84

Name:

Oxidoreductase

Title:

Hdbt inhibited yeast cytochrome bc1 complex

Structure:

Ubiquinol-cytochromE C reductase complex core protein i. Chain: a. Ubiquinol-cytochromE C reductase complex core protein 2. Chain: b. Cytochrome b. Chain: c. Cytochrome c1, heme protein.

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 PDB file)

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:

2.50Å

R-factor:

0.228

R-free:

0.252

Authors:

H.Palsdottir,C.G.Lojero,B.L.Trumpower,C.Hunte

Key ref:

H.Palsdottir et al. (2003). Structure of the yeast cytochrome bc1 complex with a hydroxyquinone anion Qo site inhibitor bound.. J Biol Chem, 278, 31303-31311. [PubMed id: 12782631] [DOI: 10.1074/jbc.M302195200]

Date:

06-May-03

Release date:

29-Jul-03

Related entries:

1kb9
tightly bound phospholipids in stigmatellin inhibited
cytochrome bc1 complex, ubiquinone at qi site, fv fragment
1ezv
stigmatellin inhibited cytochrome bc1 complex, ubiquinone
at qi site, fv fragment
1kyo
cytochromE C bound to yeast cytochrome bc1 complex, fv
fragment

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Key reference

DOI no: 10.1074/jbc.M302195200

J Biol Chem 278:31303-31311 (2003)

PubMed id: 12782631

Structure of the yeast cytochrome bc1 complex with a hydroxyquinone anion Qo site inhibitor bound.

H.Palsdottir, C.G.Lojero, B.L.Trumpower, C.Hunte.

ABSTRACT

Bifurcated electron transfer during ubiquinol oxidation is the key reaction of cytochrome bc1 complex catalysis. Binding of the competitive inhibitor 5-n-heptyl-6-hydroxy-4,7-dioxobenzothiazole to the Qo site of the cytochrome bc1 complex from Saccharomyces cerevisiae was analyzed by x-ray crystallography. This alkylhydroxydioxobenzothiazole is bound in its ionized form as evident from the crystal structure and confirmed by spectroscopic analysis, consistent with a measured pKa = 6.1 of the hydroxy group in detergent micelles. Stabilizing forces for the hydroxyquinone anion inhibitor include a polarized hydrogen bond to the iron-sulfur cluster ligand His181 and on-edge interactions via weak hydrogen bonds with cytochrome b residue Tyr279. The hydroxy group of the latter contributes to stabilization of the Rieske protein in the b-position by donating a hydrogen bond. The reported pH dependence of inhibition with lower efficacy at alkaline pH is attributed to the protonation state of His181 with a pKa of 7.5. Glu272, a proposed primary ligand and proton acceptor of ubiquinol, is not bound to the carbonyl group of the hydroxydioxobenzothiazole ring but is rotated out of the binding pocket toward the heme bL propionate A, to which it is hydrogen-bonded via a single water molecule. The observed hydrogen bonding pattern provides experimental evidence for the previously proposed proton exit pathway involving the heme propionate and a chain of water molecules. Binding of the alkyl-6-hydroxy-4,7-dioxobenzothiazole is discussed as resembling an intermediate step of ubiquinol oxidation, supporting a single occupancy model at the Qo site.

Selected figure(s)

Figure 1.
FIG. 1. The structure of the dimeric bc[1] complex depicted as a ribbon diagram. Ligands are shown as ball and stick models. HHDBT (yellow) is bound at the Q[o] site between the [2Fe-2S] cluster and the heme b[L]. Tightly bound phospholipid molecules (gray) are mainly present in the matrix-oriented leaflet of the phospholipid bilayer. The newly identified phosphatidylcholine molecule (PC, dark gray) at the intermembrane side marks the position of the enzyme with respect to the bilayer.

Figure 6.
FIG. 6. Apparent hydrogen bond network at the Q[o] site with the hydroxyquinone anion inhibitor bound. Glu272 is hydrogen-bonded to the heme b[L] propionate A, from which a proton exit pathway is formed by a chain of hydrogen-bonded water molecules, as depicted with the dotted lines. The arrow from Wat274 shows the proton exit pathway to bulk solvent. Hydrogen bonds stabilizing the ligand are shown as stippled lines. The position of Glu272 in the stigmatellin-inhibited bc[1] complex is indicated in yellow.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 31303-31311) copyright 2003.

Figures were selected by the author.