PDBsum entry: 1ntk

Oxidoreductase

PDB-id

1ntk


	Asymmetric unit

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Contents

Description

Header details

Protein chains

Ligands

HEM ×3

AY1

FES

Waters ×342

* Residue conservation analysis

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

PDB id:

1ntk

Name:

Oxidoreductase

Title:

Crystal structure of mitochondrial cytochrome bc1 in complex with antimycin a1

Structure:

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

Source:

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

Biological unit:

22mer (from PDB file)

UniProt:

Chain A: P31800 (QCR1_BOVIN)

Seq:

Struc:


Seq:				480 a.a.

Struc:				446 a.a.

Chain B: P23004 (QCR2_BOVIN)

Seq:

Struc:


Seq:				453 a.a.

Struc:				423 a.a.

Chain C: P00157 (CYB_BOVIN)

Seq:

Struc:


Seq:				379 a.a.

Struc:				378 a.a.

Chain D: P00125 (CY1_BOVIN)

Seq:

Struc:


Seq:				325 a.a.

Struc:				241 a.a.

Chain E: P13272 (UCRI_BOVIN)

Seq:

Struc:


Seq:				274 a.a.

Struc:				196 a.a.

Chain F: P00129 (QCR7_BOVIN)

Seq:				111 a.a.

Struc:				105 a.a.*

Chain G: P13271 (QCR8_BOVIN)

Seq:				82 a.a.

Struc:				79 a.a.

Chain H: P00126 (QCR6_BOVIN)

Seq:				91 a.a.

Struc:				76 a.a.

Chain I: P13272 (UCRI_BOVIN)

Seq:

Struc:


Seq:				274 a.a.

Struc:				57 a.a.

Chain J: P00130 (QCR9_BOVIN)

Seq:				64 a.a.

Struc:				60 a.a.

Chain K: P07552 (QCR10_BOVIN)

Seq:

56 a.a.

Struc:

53 a.a.*

Key:		PfamA domain
		Secondary structure			CATH domain

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

Enzyme class:

Chains E, I: 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:

2.60Å

R-factor:

0.234

R-free:

0.270

Authors:

X.Gao,X.Wen,L.Esser,B.Quinn,L.Yu,C.-A.Yu,D.Xia

Key ref:

X.Gao et al. (2003). Structural basis for the quinone reduction in the bc1 complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc1 with bound substrate and inhibitors at the Qi site.. Biochemistry, 42, 9067-9080. [PubMed id: 12885240] [DOI: 10.1021/bi0341814]

Date:

30-Jan-03

Release date:

07-Oct-03

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Enzyme reaction for E.C.1.10.2.2

QH(2)

2 × ferricytochrome c

2 × ferrocytochrome c
Bound ligand (Het Group name = HEM)
matches with 70.00% similarity

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

Key reference

DOI no: 10.1021/bi0341814 Biochemistry 42:9067-9080 (2003)

PubMed id: 12885240

Structural basis for the quinone reduction in the bc1 complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc1 with bound substrate and inhibitors at the Qi site.

X.Gao, X.Wen, L.Esser, B.Quinn, L.Yu, C.A.Yu, D.Xia.

ABSTRACT

Cytochrome bc(1) is an integral membrane protein complex essential to cellular respiration and photosynthesis. The Q cycle reaction mechanism of bc(1) postulates a separated quinone reduction (Q(i)) and quinol oxidation (Q(o)) site. In a complete catalytic cycle, a quinone molecule at the Q(i) site receives two electrons from the b(H) heme and two protons from the negative side of the membrane; this process is specifically inhibited by antimycin A and NQNO. The structures of bovine mitochondrial bc(1) in the presence or absence of bound substrate ubiquinone and with either the bound antimycin A(1) or NQNO were determined and refined. A ubiquinone with its first two isoprenoid repeats and an antimycin A(1) were identified in the Q(i) pocket of the substrate and inhibitor bound structures, respectively; the NQNO, on the other hand, was identified in both Q(i) and Q(o) pockets in the inhibitor complex. The two inhibitors occupied different portions of the Q(i) pocket and competed with substrate for binding. In the Q(o) pocket, the NQNO behaves similarly to stigmatellin, inducing an iron-sulfur protein conformational arrest. Extensive binding interactions and conformational adjustments of residues lining the Q(i) pocket provide a structural basis for the high affinity binding of antimycin A and for phenotypes of inhibitor resistance. A two-water-mediated ubiquinone protonation mechanism is proposed involving three Q(i) site residues His(201), Lys(227), and Asp(228).

Literature references that cite this PDB file's key reference

PubMed id Reference

19219048 A.Guskov, J.Kern, A.Gabdulkhakov, M.Broser, A.Zouni, and W.Saenger (2009).
Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride.

Nat Struct Mol Biol, 16, 334-342.

PDB codes: 3bz1 3bz2

19415898 M.Sarewicz, M.Dutka, W.Froncisz, and A.Osyczka (2009).
Magnetic interactions sense changes in distance between heme b(L) and the iron-sulfur cluster in cytochrome bc(1).

Biochemistry, 48, 5708-5720.

19774111 Q.L.Chen, X.S.Tang, W.J.Yao, and S.Q.Lu (2009).
Bioinformatics analysis of the complete sequences of cytochrome b of Takydromus sylvaticus and modeling the tertiary structure of encoded protein.

Int J Biol Sci, 5, 596-602.

19503808 W.A.Beckstead, M.T.Ebbert, M.J.Rowe, and D.A.McClellan (2009).
Evolutionary pressure on mitochondrial cytochrome b is consistent with a role of CytbI7T affecting longevity during caloric restriction.

PLoS One, 4, e5836.

18766386 Y.El Khoury, and P.Hellwig (2009).
Infrared spectroscopic characterization of copper-polyhistidine from 1,800 to 50 cm(-1): model systems for copper coordination.

J Biol Inorg Chem, 14, 23-34.

18701458 B.Gurung, L.Yu, and C.A.Yu (2008).
Stigmatellin Induces Reduction of Iron-Sulfur Protein in the Oxidized Cytochrome bc1 Complex.

J Biol Chem, 283, 28087-28094.

18418633 E.A.Berry, and F.A.Walker (2008).
Bis-histidine-coordinated hemes in four-helix bundles: how the geometry of the bundle controls the axial imidazole plane orientations in transmembrane cytochromes of mitochondrial complexes II and III and related proteins.

J Biol Inorg Chem, 13, 481-498.

18039651 L.Esser, M.Elberry, F.Zhou, C.A.Yu, L.Yu, and D.Xia (2008).
Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides.

J Biol Chem, 283, 2846-2857.

PDB codes: 2qjk 2qjp 2qjy

18956237 S.E.Chobot, H.Zhang, C.C.Moser, and P.L.Dutton (2008).
Breaking the Q-cycle: finding new ways to study Qo through thermodynamic manipulations.

J Bioenerg Biomembr, 40, 501-507.

17369262 A.M.James, M.S.Sharpley, A.R.Manas, F.E.Frerman, J.Hirst, R.A.Smith, and M.P.Murphy (2007).
Interaction of the mitochondria-targeted antioxidant MitoQ with phospholipid bilayers and ubiquinone oxidoreductases.

J Biol Chem, 282, 14708-14718.

17200733 A.Y.Mulkidjanian (2007).
Proton translocation by the cytochrome bc1 complexes of phototrophic bacteria: introducing the activated Q-cycle.

Photochem Photobiol Sci, 6, 19-34.

17457691 D.Xia, L.Esser, L.Yu, and C.A.Yu (2007).
Structural basis for the mechanism of electron bifurcation at the quinol oxidation site of the cytochrome bc1 complex.

Photosynth Res, 92, 17-34.

17360398 J.Zhu, T.Egawa, S.R.Yeh, L.Yu, and C.A.Yu (2007).
Simultaneous reduction of iron-sulfur protein and cytochrome b(L) during ubiquinol oxidation in cytochrome bc(1) complex.

Proc Natl Acad Sci U S A, 104, 4864-4869.

17573435 L.Giachini, F.Francia, G.Veronesi, D.W.Lee, F.Daldal, L.S.Huang, E.A.Berry, T.Cocco, S.Papa, F.Boscherini, and G.Venturoli (2007).
X-Ray absorption studies of Zn2+ binding sites in bacterial, avian, and bovine cytochrome bc1 complexes.

Biophys J, 93, 2934-2951.

17616531 S.A.Dikanov, J.T.Holland, B.Endeward, D.R.Kolling, R.I.Samoilova, T.F.Prisner, and A.R.Crofts (2007).
Hydrogen bonds between nitrogen donors and the semiquinone in the Qi-site of the bc1 complex.

J Biol Chem, 282, 25831-25841.

17213201 S.B.Le, M.K.Hailer, S.Buhrow, Q.Wang, K.Flatten, P.Pediaditakis, K.C.Bible, L.D.Lewis, E.A.Sausville, Y.P.Pang, M.M.Ames, J.J.Lemasters, E.L.Holmuhamedov, and S.H.Kaufmann (2007).
Inhibition of mitochondrial respiration as a source of adaphostin-induced reactive oxygen species and cytotoxicity.

J Biol Chem, 282, 8860-8872.

16829675 E.Maklashina, P.Hellwig, R.A.Rothery, V.Kotlyar, Y.Sher, J.H.Weiner, and G.Cecchini (2006).
Differences in protonation of ubiquinone and menaquinone in fumarate reductase from Escherichia coli.

J Biol Chem, 281, 26655-26664.

16586113 F.A.Walker (2006).
The heme environment of mouse neuroglobin: histidine imidazole plane orientations obtained from solution NMR and EPR spectroscopy as compared with X-ray crystallography.

J Biol Inorg Chem, 11, 391-397.

16671046 H.B.Yi, M.Diefenbach, Y.C.Choi, E.C.Lee, H.M.Lee, B.H.Hong, and K.S.Kim (2006).
Interactions of neutral and cationic transition metals with the redox system of hydroquinone and quinone: theoretical characterization of the binding topologies, and implications for the formation of nanomaterials.

Chemistry, 12, 4885-4892.

16371475 J.Yan, G.Kurisu, and W.A.Cramer (2006).
Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex.

Proc Natl Acad Sci U S A, 103, 69-74.

16924113 L.Esser, X.Gong, S.Yang, L.Yu, C.A.Yu, and D.Xia (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.

PDB codes: 2fyn 2fyu

16987808 M.G.Ding, J.P.di Rago, and B.L.Trumpower (2006).
Investigating the Qn site of the cytochrome bc1 complex in Saccharomyces cerevisiae with mutants resistant to ilicicolin H, a novel Qn site inhibitor.

J Biol Chem, 281, 36036-36043.

16825195 S.Chatterjee, P.Home, S.Mukherjee, B.Mahata, S.Goswami, G.Dhar, and S.Adhya (2006).
An RNA-binding respiratory component mediates import of type II tRNAs into Leishmania mitochondria.

J Biol Chem, 281, 25270-25277.

16756511 W.A.Cramer, H.Zhang, J.Yan, G.Kurisu, and J.L.Smith (2006).
Transmembrane traffic in the cytochrome b6f complex.

Annu Rev Biochem, 75, 769-790.

15788391 A.M.James, H.M.Cochemé, R.A.Smith, and M.P.Murphy (2005).
Interactions of mitochondria-targeted and untargeted ubiquinones with the mitochondrial respiratory chain and reactive oxygen species. Implications for the use of exogenous ubiquinones as therapies and experimental tools.

J Biol Chem, 280, 21295-21312.

15878858 B.Gurung, L.Yu, D.Xia, and C.A.Yu (2005).
The iron-sulfur cluster of the Rieske iron-sulfur protein functions as a proton-exiting gate in the cytochrome bc(1) complex.

J Biol Chem, 280, 24895-24902.

15632120 M.E.Nelson, G.Finazzi, Q.J.Wang, K.A.Middleton-Zarka, J.Whitmarsh, and T.Kallas (2005).
Cytochrome b6 arginine 214 of Synechococcus sp. PCC 7002, a key residue for quinone-reductase site function and turnover of the cytochrome bf complex.

J Biol Chem, 280, 10395-10402.

14977419 A.R.Crofts (2004).
The cytochrome bc1 complex: function in the context of structure.

Annu Rev Physiol, 66, 689-733.

14736869 S.A.Dikanov, R.I.Samoilova, D.R.Kolling, J.T.Holland, and A.R.Crofts (2004).
Hydrogen bonds involved in binding the Qi-site semiquinone in the bc1 complex, identified through deuterium exchange using pulsed EPR.

J Biol Chem, 279, 15814-15823.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.