PDBsum entry 1qle

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase/immune system PDB id
Protein chains
538 a.a. *
252 a.a. *
273 a.a. *
43 a.a. *
119 a.a. *
108 a.a. *
PC1 ×2
HEA ×2
* Residue conservation analysis
PDB id:
Name: Oxidoreductase/immune system
Title: Cryo-structure of the paracoccus denitrificans four-subunit cytochromE C oxidase in the completely oxidized state complexed with an antibody fv fragment
Structure: CytochromE C oxidase polypeptide i-beta. Chain: a. Synonym: cytochrome aa3 subunit 1-beta. CytochromE C oxidase polypeptide ii. Chain: b. Synonym: cytochrome aa3 subunit 2, oxidase aa(3) subunit 2. CytochromE C oxidase polypeptide iii. Chain: c. Synonym: cytochrome aa3subunit 3, oxidase aa(3) subunit 3.
Source: Paracoccus denitrificans. Organism_taxid: 266. Atcc: 13543. Cellular_location: cytoplasmic membrane. Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
3.0Å     R-factor:   0.235     R-free:   0.309
Authors: A.Harrenga,H.Michel
Key ref:
A.Harrenga and H.Michel (1999). The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction. J Biol Chem, 274, 33296-33299. PubMed id: 10559205 DOI: 10.1074/jbc.274.47.33296
30-Aug-99     Release date:   02-Dec-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P98002  (COX1B_PARDE) -  Cytochrome c oxidase subunit 1-beta
558 a.a.
538 a.a.
Protein chain
Pfam   ArchSchema ?
P08306  (COX2_PARDE) -  Cytochrome c oxidase subunit 2
298 a.a.
252 a.a.
Protein chain
Pfam   ArchSchema ?
P06030  (COX3_PARDE) -  Cytochrome c oxidase subunit 3
274 a.a.
273 a.a.
Protein chain
Pfam   ArchSchema ?
P77921  (COX4_PARDE) -  Cytochrome c oxidase subunit 4
50 a.a.
43 a.a.
Protein chain
No UniProt id for this chain
Struc: 119 a.a.
Protein chain
No UniProt id for this chain
Struc: 108 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.  - Cytochrome-c oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
4 × ferrocytochrome c
Bound ligand (Het Group name = HEA)
matches with 50.00% similarity
+ O(2)
+ 4 × H(+)
= 4 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Copper
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     oxidation-reduction process   14 terms 
  Biochemical function     electron carrier activity     8 terms  


DOI no: 10.1074/jbc.274.47.33296 J Biol Chem 274:33296-33299 (1999)
PubMed id: 10559205  
The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction.
A.Harrenga, H.Michel.
Cytochrome c oxidase catalyzes the reduction of oxygen to water. This process is accompanied by the vectorial transport of protons across the mitochondrial or bacterial membrane ("proton pumping"). The mechanism of proton pumping is still a matter of debate. Many proposed mechanisms require structural changes during the reaction cycle of cytochrome c oxidase. Therefore, the structure of the cytochrome c oxidase was determined in the completely oxidized and in the completely reduced states at a temperature of 100 K. No ligand exchanges or other major structural changes upon reduction of the cytochrome c oxidase from Paracoccus denitrificans were observed. The three histidine Cu(B) ligands are well defined in the oxidized and in the reduced states. These results are hardly compatible with the "histidine cycle" mechanisms formulated previously.
  Selected figure(s)  
Figure 1.
Fig. 1. Single crystal microspectrophotometry of air oxidized (thick solid curve), dithionite reduced (thin solid curve), and reduced carbon monoxide-treated (dashed curve) cytochrome c oxidase crystals from P. denitrificans. A shows the absolute spectra and B the difference spectra between dithionite reduced and air oxidized crystals.
Figure 2.
Fig. 2. Simulated annealing omit electron density maps (19) of Cu[B] and the three histidine ligands (counter level 1 ) for the oxidized cytochrome c oxidase measured at 100 K (A) and the dithionite reduced cytochrome c oxidase measured at 100 K (B). The electron density maps are superimposed on the refined models.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 33296-33299) copyright 1999.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205904 J.Liu, L.Qin, and S.Ferguson-Miller (2011).
Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.
  Proc Natl Acad Sci U S A, 108, 1284-1289.
PDB codes: 3om3 3oma 3omi 3omn
20715054 Y.Mokrab, T.J.Stevens, and K.Mizuguchi (2010).
A structural dissection of amino acid substitutions in helical transmembrane proteins.
  Proteins, 78, 2895-2907.  
19244388 A.Lo, Y.Y.Chiu, E.A.Rødland, P.C.Lyu, T.Y.Sung, and W.L.Hsu (2009).
Predicting helix-helix interactions from residue contacts in membrane proteins.
  Bioinformatics, 25, 996.  
19140675 B.Liu, Y.Chen, T.Doukov, S.M.Soltis, C.D.Stout, and J.A.Fee (2009).
Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme.
  Biochemistry, 48, 820-826.
PDB codes: 3eh3 3eh4 3eh5
19770503 C.A.Kors, E.Wallace, D.R.Davies, L.Li, P.D.Laible, and P.Nollert (2009).
Effects of impurities on membrane-protein crystallization in different systems.
  Acta Crystallogr D Biol Crystallogr, 65, 1062-1073.  
19397279 L.Qin, J.Liu, D.A.Mills, D.A.Proshlyakov, C.Hiser, and S.Ferguson-Miller (2009).
Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake.
  Biochemistry, 48, 5121-5130.
PDB codes: 3fye 3fyi
19416061 S.Raunser, and T.Walz (2009).
Electron crystallography as a technique to study the structure on membrane proteins in a lipidic environment.
  Annu Rev Biophys, 38, 89.  
17949262 I.Belevich, and M.I.Verkhovsky (2008).
Molecular mechanism of proton translocation by cytochrome C oxidase.
  Antioxid Redox Signal, 10, 1.  
18928258 J.A.Fee, D.A.Case, and L.Noodleman (2008).
Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: application of density functional theory to cytochrome ba3 of Thermus thermophilus.
  J Am Chem Soc, 130, 15002-15021.  
18541140 R.Sugitani, E.S.Medvedev, and A.A.Stuchebrukhov (2008).
Theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme.
  Biochim Biophys Acta, 1777, 1129-1139.  
17514341 C.Dallacosta, W.A.Alves, A.M.da Costa Ferreira, E.Monzani, and L.Casella (2007).
A new dinuclear heme-copper complex derived from functionalized protoporphyrin IX.
  Dalton Trans, (), 2197-2206.  
17332748 K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, and S.Yoshikawa (2007).
Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase.
  EMBO J, 26, 1713-1725.
PDB codes: 2dyr 2dys
17719219 L.Qin, M.A.Sharpe, R.M.Garavito, and S.Ferguson-Miller (2007).
Conserved lipid-binding sites in membrane proteins: a focus on cytochrome c oxidase.
  Curr Opin Struct Biol, 17, 444-450.  
16387770 O.Farver, E.Grell, B.Ludwig, H.Michel, and I.Pecht (2006).
Rates and Equilibrium of CuA to heme a electron transfer in Paracoccus denitrificans cytochrome c oxidase.
  Biophys J, 90, 2131-2137.  
16172928 A.J.Watson, A.V.Hughes, P.K.Fyfe, M.C.Wakeham, K.Holden-Dye, P.Heathcote, and M.R.Jones (2005).
On the role of basic residues in adapting the reaction centre-LH1 complex for growth at elevated temperatures in purple bacteria.
  Photosynth Res, 86, 81.  
15583964 R.A.Ghiladi, H.W.Huang, P.Moënne-Loccoz, J.Stasser, N.J.Blackburn, A.S.Woods, R.J.Cotter, C.D.Incarvito, A.L.Rheingold, and K.D.Karlin (2005).
Heme-copper/dioxygen adduct formation relevant to cytochrome c oxidase: spectroscopic characterization of [(6L)FeIII-(O2(2-))-CuII]+.
  J Biol Inorg Chem, 10, 63-77.  
16163550 T.M.Bandeiras, M.M.Pereira, M.Teixeira, P.Moenne-Loccoz, and N.J.Blackburn (2005).
Structure and coordination of CuB in the Acidianus ambivalens aa3 quinol oxidase heme-copper center.
  J Biol Inorg Chem, 10, 625-635.  
15240491 D.A.Svistunenko, and C.E.Cooper (2004).
A new method of identifying the site of tyrosyl radicals in proteins.
  Biophys J, 87, 582-595.  
15313235 E.Pebay-Peyroula, and G.Brandolin (2004).
Nucleotide exchange in mitochondria: insight at a molecular level.
  Curr Opin Struct Biol, 14, 420-425.  
14604533 E.Balatri, L.Banci, I.Bertini, F.Cantini, and S.Ciofi-Baffoni (2003).
Solution structure of Sco1: a thioredoxin-like protein Involved in cytochrome c oxidase assembly.
  Structure, 11, 1431-1443.
PDB code: 1on4
14603310 E.Pebay-Peyroula, C.Dahout-Gonzalez, R.Kahn, V.Trézéguet, G.J.Lauquin, and G.Brandolin (2003).
Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside.
  Nature, 426, 39-44.
PDB code: 1okc
12657787 L.O.Essen, A.Harrenga, C.Ostermeier, and H.Michel (2003).
1.3 A X-ray structure of an antibody Fv fragment used for induced membrane-protein crystallization.
  Acta Crystallogr D Biol Crystallogr, 59, 677-687.
PDB code: 1mqk
14645072 S.J.Alvis, I.M.Williamson, J.M.East, and A.G.Lee (2003).
Interactions of anionic phospholipids and phosphatidylethanolamine with the potassium channel KcsA.
  Biophys J, 85, 3828-3838.  
12167672 A.Camara-Artigas, D.Brune, and J.P.Allen (2002).
Interactions between lipids and bacterial reaction centers determined by protein crystallography.
  Proc Natl Acad Sci U S A, 99, 11055-11060.
PDB code: 1m3x
12163074 C.Hunte, and H.Michel (2002).
Crystallisation of membrane proteins mediated by antibody fragments.
  Curr Opin Struct Biol, 12, 503-508.  
11870867 D.Flöck, and V.Helms (2002).
Protein--protein docking of electron transfer complexes: cytochrome c oxidase and cytochrome c.
  Proteins, 47, 75-85.  
11948164 K.M.Jones, and R.Haselkorn (2002).
Newly identified cytochrome c oxidase operon in the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 specifically induced in heterocysts.
  J Bacteriol, 184, 2491-2499.  
11340051 B.E.Schultz, and S.I.Chan (2001).
Structures and proton-pumping strategies of mitochondrial respiratory enzymes.
  Annu Rev Biophys Biomol Struct, 30, 23-65.  
11341911 J.Abramson, M.Svensson-Ek, B.Byrne, and S.Iwata (2001).
Structure of cytochrome c oxidase: a comparison of the bacterial and mitochondrial enzymes.
  Biochim Biophys Acta, 1544, 1-9.  
11166568 P.K.Fyfe, K.E.McAuley, A.W.Roszak, N.W.Isaacs, R.J.Cogdell, and M.R.Jones (2001).
Probing the interface between membrane proteins and membrane lipids by X-ray crystallography.
  Trends Biochem Sci, 26, 106-112.  
11325707 T.K.Das, F.L.Tomson, R.B.Gennis, M.Gordon, and D.L.Rousseau (2001).
pH-dependent structural changes at the Heme-Copper binuclear center of cytochrome c oxidase.
  Biophys J, 80, 2039-2045.  
10966478 J.L.Popot, and D.M.Engelman (2000).
Helical membrane protein folding, stability, and evolution.
  Annu Rev Biochem, 69, 881-922.  
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.