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PDBsum entry 3h1k

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
3h1k
Jmol
Contents
Protein chains
443 a.a. *
426 a.a. *
380 a.a. *
241 a.a. *
196 a.a. *
101 a.a. *
80 a.a. *
69 a.a. *
46 a.a. *
61 a.a. *
Ligands
PEE ×6
UNL ×5
HEM ×4
IKR ×2
_UQ ×2
CDL ×4
GOL ×2
HEC ×2
BOG ×5
FES ×2
Metals
_ZN ×2
Waters ×17
* Residue conservation analysis
PDB id:
3h1k
Name: Oxidoreductase
Title: Chicken cytochrome bc1 complex with zn++ and an iodinated de of kresoxim-methyl bound
Structure: Mitochondrial ubiquinol-cytochromE-C reductase co protein i. Chain: a, n. Mitochondrial ubiquinol-cytochromE-C reductase co protein 2. Chain: b, o. Cytochrome b. Chain: c, p. Synonym: ubiquinol-cytochromE-C reductase complex cytochrom
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organism_taxid: 9031
Resolution:
3.48Å     R-factor:   0.239     R-free:   0.284
Authors: E.A.Berry,Z.Zhang,H.D.Bellamy,L.S.Huang
Key ref: E.A.Berry et al. (2000). Crystallographic location of two Zn(2+)-binding sites in the avian cytochrome bc(1) complex. Biochim Biophys Acta, 1459, 440-448. PubMed id: 11004461
Date:
12-Apr-09     Release date:   28-Apr-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
D0VX31  (D0VX31_CHICK) -  Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i
Seq:
Struc:
446 a.a.
443 a.a.
Protein chains
Pfam   ArchSchema ?
D0VX29  (D0VX29_CHICK) -  Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2
Seq:
Struc:
441 a.a.
426 a.a.
Protein chains
Pfam   ArchSchema ?
P18946  (CYB_CHICK) -  Cytochrome b
Seq:
Struc:
380 a.a.
380 a.a.
Protein chains
Pfam   ArchSchema ?
D0VX26  (D0VX26_CHICK) -  Mitochondrial cytochrome c1, heme protein
Seq:
Struc:
241 a.a.
241 a.a.
Protein chains
Pfam   ArchSchema ?
Q5ZLR5  (UCRI_CHICK) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
272 a.a.
196 a.a.
Protein chains
Pfam   ArchSchema ?
D0VX30  (D0VX30_CHICK) -  Cytochrome b-c1 complex subunit 7
Seq:
Struc:
110 a.a.
101 a.a.
Protein chains
Pfam   ArchSchema ?
D0VX32  (D0VX32_CHICK) -  Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c
Seq:
Struc:
81 a.a.
80 a.a.
Protein chains
Pfam   ArchSchema ?
D0VX28  (D0VX28_CHICK) -  Cytochrome b-c1 complex subunit 6
Seq:
Struc:
77 a.a.
69 a.a.
Protein chains
Pfam   ArchSchema ?
Q5ZLR5  (UCRI_CHICK) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
272 a.a.
46 a.a.*
Protein chains
Pfam   ArchSchema ?
D0VX27  (D0VX27_CHICK) -  Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein
Seq:
Struc:
61 a.a.
61 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 15 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, D, E, G, I, J, N, O, Q, R, T, V, W: E.C.1.10.2.2  - Quinol--cytochrome-c reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H+
Quinol
Bound ligand (Het Group name = UQ)
matches with 82.61% similarity
+
2 × ferricytochrome c
Bound ligand (Het Group name = HEM)
matches with 63.64% similarity
= quinone
+ 2 × ferrocytochrome c
+ 2 × H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   8 terms 
  Biological process     mitochondrial electron transport, ubiquinol to cytochrome c   5 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
Biochim Biophys Acta 1459:440-448 (2000)
PubMed id: 11004461  
 
 
Crystallographic location of two Zn(2+)-binding sites in the avian cytochrome bc(1) complex.
E.A.Berry, Z.Zhang, H.D.Bellamy, L.Huang.
 
  ABSTRACT  
 
The chicken mitochondrial ubiquinol cytochrome c oxidoreductase (bc(1) complex) is inhibited by Zn(2+) ions, but with higher K(i) ( approximately 3 microM) than the corresponding bovine enzyme. When equilibrated with mother liquor containing 200 microM ZnCl(2) for 7 days, the crystalline chicken bc(1) complex specifically binds Zn(2+) at 4 sites representing two sites on each monomer in the dimer. These two sites are close to the stigmatellin-binding site, taken to be center Q(o) of the Q-cycle mechanism, and are candidates for the inhibitory site. One binding site is actually in the hydrophobic channel between the Q(o) site and the bulk lipid phase, and may interfere with quinone binding. The other is in a hydrophilic area between cytochromes b and c(1), and might interfere with the egress of protons from the Q(o) site to the intermembrane aqueous medium. No zinc was bound near the putative proteolytic active site of subunits 1 and 2 (homologous to mitochondrial processing peptidase) under these conditions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20029110 L.Giachini, G.Veronesi, F.Francia, G.Venturoli, and F.Boscherini (2010).
Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins.
  J Synchrotron Radiat, 17, 41-52.  
19089881 S.G.Bell, and B.L.Vallee (2009).
The metallothionein/thionein system: an oxidoreductive metabolic zinc link.
  Chembiochem, 10, 55-62.  
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.  
17470809 K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-o, E.Yamashita, H.Aoyama, T.Tsukihara, and S.Yoshikawa (2007).
A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 104, 7881-7886.
PDB codes: 2eij 2eik 2eil 2eim 2ein
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.  
17477548 L.Qin, D.A.Mills, C.Hiser, A.Murphree, R.M.Garavito, S.Ferguson-Miller, and J.Hosler (2007).
Crystallographic location and mutational analysis of Zn and Cd inhibitory sites and role of lipidic carboxylates in rescuing proton path mutants in cytochrome c oxidase.
  Biochemistry, 46, 6239-6248.  
16756489 J.P.Hosler, S.Ferguson-Miller, and D.A.Mills (2006).
Energy transduction: proton transfer through the respiratory complexes.
  Annu Rev Biochem, 75, 165-187.  
16980308 M.S.Sharpley, and J.Hirst (2006).
The inhibition of mitochondrial complex I (NADH:ubiquinone oxidoreductase) by Zn2+.
  J Biol Chem, 281, 34803-34809.  
16987000 W.Maret (2006).
Zinc coordination environments in proteins as redox sensors and signal transducers.
  Antioxid Redox Signal, 8, 1419-1441.  
15613631 L.Giachini, F.Francia, A.Mallardi, G.Palazzo, E.Carpenè, F.Boscherini, and G.Venturoli (2005).
Multiple scattering x-ray absorption studies of Zn2+ binding sites in bacterial photosynthetic reaction centers.
  Biophys J, 88, 2038-2046.  
15807649 S.S.Kuznetsova, N.V.Azarkina, T.V.Vygodina, S.A.Siletsky, and A.A.Konstantinov (2005).
Zinc ions as cytochrome C oxidase inhibitors: two sites of action.
  Biochemistry (Mosc), 70, 128-136.  
11900550 A.G.Roberts, M.K.Bowman, and D.M.Kramer (2002).
Certain metal ions are inhibitors of cytochrome b6f complex 'Rieske' iron-sulfur protein domain movements.
  Biochemistry, 41, 4070-4079.  
  11832490 D.A.Mills, B.Schmidt, C.Hiser, E.Westley, and S.Ferguson-Miller (2002).
Membrane potential-controlled inhibition of cytochrome c oxidase by zinc.
  J Biol Chem, 277, 14894-14901.  
11744691 I.G.Gazaryan, B.F.Krasnikov, G.A.Ashby, R.N.Thorneley, B.S.Kristal, and A.M.Brown (2002).
Zinc is a potent inhibitor of thiol oxidoreductase activity and stimulates reactive oxygen species production by lipoamide dehydrogenase.
  J Biol Chem, 277, 10064-10072.  
11226237 B.Ye, W.Maret, and B.L.Vallee (2001).
Zinc metallothionein imported into liver mitochondria modulates respiration.
  Proc Natl Acad Sci U S A, 98, 2317-2322.  
11722564 R.Covián, and R.Moreno-Sánchez (2001).
Role of protonatable groups of bovine heart bc(1) complex in ubiquinol binding and oxidation.
  Eur J Biochem, 268, 5783-5790.  
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.