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Oxidoreductase PDB id
1ocz
Jmol
Contents
Protein chains
514 a.a. *
227 a.a. *
261 a.a. *
144 a.a. *
109 a.a. *
98 a.a. *
84 a.a. *
75 a.a. *
73 a.a. *
56 a.a. *
49 a.a. *
47 a.a. *
43 a.a. *
Ligands
AZI ×4
HEA ×4
Metals
_CU ×6
_ZN ×2
_MG ×2
_NA ×2
* Residue conservation analysis
PDB id:
1ocz
Name: Oxidoreductase
Title: Bovine heart cytochromE C oxidase in azide-bound state
Structure: CytochromE C oxidase. Chain: a, n. Synonym: ferrocytochrome c\:oxygen oxidoreductase. Other_details: this enzyme is a hybrid protein complex and is a homodimer. Azide-bound state.. CytochromE C oxidase. Chain: b, o. Synonym: ferrocytochrome c\:oxygen oxidoreductase. Other_details: this enzyme is a hybrid protein complex and
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: heart. Tissue: heart muscle. Organelle: mitochondrion. Organelle: mitochondrion
Biol. unit: 26mer (from PQS)
Resolution:
2.90Å     R-factor:   0.195     R-free:   0.255
Authors: T.Tsukihara,M.Yao
Key ref:
S.Yoshikawa et al. (1998). Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. Science, 280, 1723-1729. PubMed id: 9624044 DOI: 10.1126/science.280.5370.1723
Date:
13-Jul-98     Release date:   22-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00396  (COX1_BOVIN) -  Cytochrome c oxidase subunit 1
Seq:
Struc: 		514 a.a.
514 a.a.
Protein chains
Pfam   ArchSchema ?
P68530  (COX2_BOVIN) -  Cytochrome c oxidase subunit 2
Seq:
Struc: 		227 a.a.
227 a.a.
Protein chains
Pfam   ArchSchema ?
P00415  (COX3_BOVIN) -  Cytochrome c oxidase subunit 3
Seq:
Struc: 		261 a.a.
261 a.a.*
Protein chains
Pfam   ArchSchema ?
P00423  (COX41_BOVIN) -  Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Seq:
Struc: 		169 a.a.
144 a.a.
Protein chains
Pfam   ArchSchema ?
P00426  (COX5A_BOVIN) -  Cytochrome c oxidase subunit 5A, mitochondrial
Seq:
Struc: 		152 a.a.
109 a.a.
Protein chains
Pfam   ArchSchema ?
P00428  (COX5B_BOVIN) -  Cytochrome c oxidase subunit 5B, mitochondrial
Seq:
Struc: 		129 a.a.
98 a.a.
Protein chains
Pfam   ArchSchema ?
P07471  (CX6A2_BOVIN) -  Cytochrome c oxidase subunit 6A2, mitochondrial
Seq:
Struc: 		97 a.a.
84 a.a.
Protein chains
Pfam   ArchSchema ?
P00429  (CX6B1_BOVIN) -  Cytochrome c oxidase subunit 6B1
Seq:
Struc: 		86 a.a.
75 a.a.
Protein chains
Pfam   ArchSchema ?
P04038  (COX6C_BOVIN) -  Cytochrome c oxidase subunit 6C
Seq:
Struc: 		74 a.a.
73 a.a.
Protein chains
Pfam   ArchSchema ?
P07470  (CX7A1_BOVIN) -  Cytochrome c oxidase subunit 7A1, mitochondrial
Seq:
Struc: 		80 a.a.
56 a.a.
Protein chains
Pfam   ArchSchema ?
P13183  (COX7B_BOVIN) -  Cytochrome c oxidase subunit 7B, mitochondrial
Seq:
Struc: 		80 a.a.
49 a.a.
Protein chains
Pfam   ArchSchema ?
P00430  (COX7C_BOVIN) -  Cytochrome c oxidase subunit 7C, mitochondrial
Seq:
Struc: 		63 a.a.
47 a.a.
Protein chains
Pfam   ArchSchema ?
P10175  (COX8B_BOVIN) -  Cytochrome c oxidase subunit 8B, mitochondrial
Seq:
Struc: 		70 a.a.
43 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, N: E.C.1.9.3.1  - 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   9 terms 
  Biological process     oxidation-reduction process   6 terms 
  Biochemical function     electron carrier activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.280.5370.1723 Science 280:1723-1729 (1998)
PubMed id: 9624044  
 
 
Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.
S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara.
 
  ABSTRACT  
 
Crystal structures of bovine heart cytochrome c oxidase in the fully oxidized, fully reduced, azide-bound, and carbon monoxide-bound states were determined at 2.30, 2.35, 2.9, and 2.8 angstrom resolution, respectively. An aspartate residue apart from the O2 reduction site exchanges its effective accessibility to the matrix aqueous phase for one to the cytosolic phase concomitantly with a significant decrease in the pK of its carboxyl group, on reduction of the metal sites. The movement indicates the aspartate as the proton pumping site. A tyrosine acidified by a covalently linked imidazole nitrogen is a possible proton donor for the O2 reduction by the enzyme.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Crystal structures of the Fe[a3]-Cu[B] site in the fully reduced CO-bound and fully oxidized azide-bound states and those of^ the Na^+/Ca^2+ and Mg^2+ sites. (F[o] F[c]) difference Fourier maps for CO bound at Fe[a3]^ at 3 level (A) and azide bridging between Fe[a3] and Cu[B]^ at 2.2 level (B) are given where the bound ligands and^ fixed waters are not included in the F[c] calculation. The difference^ electron density maps at 4 level (1 = 0.0436e^-/Å^3) for the Na^+/Ca^2+ site (C) and for the Mg^2+ site (D). Violet, purple, and blue balls are the positions^ of Na^+, Mg^2+, and water, respectively. 		Figure 3.
Fig. 3. Redox-coupled conformational change in the segment from Gly^49 to Asn^55. The conformation of the segment in the fully oxidized form is^ stereoscopically shown in red, and that in the fully reduced form^ in green. The yellow structure denotes subunit II with no redox-coupled^ conformational change.
 
  The above figures are reprinted by permission from the AAAs: Science (1998, 280, 1723-1729) copyright 1998.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21286652 A.V.Dyuba, A.M.Arutyunyan, T.V.Vygodina, N.V.Azarkina, A.V.Kalinovich, Y.A.Sharonov, and A.A.Konstantinov (2011).
Circular dichroism spectra of cytochrome c oxidase.
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21368144 I.von der Hocht, J.H.van Wonderen, F.Hilbers, H.Angerer, F.Macmillan, and H.Michel (2011).
Interconversions of P and F intermediates of cytochrome c oxidase from Paracoccus denitrificans.
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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
21545285 S.Yoshikawa, K.Muramoto, and K.Shinzawa-Itoh (2011).
Proton-pumping mechanism of cytochrome C oxidase.
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20936199 V.L.Davidson (2011).
Generation of protein-derived redox cofactors by posttranslational modification.
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20385840 K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, and S.Yoshikawa (2010).
Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate.
  Proc Natl Acad Sci U S A, 107, 7740-7745.
PDB codes: 3ag1 3ag2 3ag3 3ag4
20667175 K.R.Vinothkumar, and R.Henderson (2010).
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20544970 L.J.Smith, A.Kahraman, and J.M.Thornton (2010).
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The mitochondrial respiratory chain.
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20380465 Z.Halime, M.T.Kieber-Emmons, M.F.Qayyum, B.Mondal, T.Gandhi, S.C.Puiu, E.E.Chufán, A.A.Sarjeant, K.O.Hodgson, B.Hedman, E.I.Solomon, and K.D.Karlin (2010).
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A spectroscopic investigation of a tridentate Cu-complex mimicking the tyrosine-histidine cross-link of cytochrome C oxidase.
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19548766 A.Y.Smirnov, L.G.Mourokh, and F.Nori (2009).
Kinetics of proton pumping in cytochrome c oxidase.
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19303362 B.Kadenbach, R.Ramzan, and S.Vogt (2009).
Degenerative diseases, oxidative stress and cytochrome c oxidase function.
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19164527 H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, and S.Yoshikawa (2009).
A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump.
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PDB codes: 2zxw 3abl 3abm
19894768 J.P.Collman, A.Dey, C.J.Barile, S.Ghosh, and R.A.Decréau (2009).
Inhibition of electrocatalytic O(2) reduction of functional CcO models by competitive, non-competitive, and mixed inhibitors.
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19541624 J.P.Collman, A.Dey, Y.Yang, S.Ghosh, and R.A.Decréau (2009).
O2 reduction by a functional heme/nonheme bis-iron NOR model complex.
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20007376 J.P.Collman, S.Ghosh, A.Dey, and R.A.Decréau (2009).
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19218360 K.Kobayashi, S.Tagawa, and T.Mogi (2009).
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19584547 K.Kobayashi, S.Tagawa, and T.Mogi (2009).
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  Biosci Biotechnol Biochem, 73, 1599-1603.  
19348907 L.Geren, B.Durham, and F.Millett (2009).
Chapter 28 Use of ruthenium photoreduction techniques to study electron transfer in cytochrome oxidase.
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19810693 M.E.Mahoney, A.Oliver, O.Einarsdóttir, and J.P.Konopelski (2009).
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19623382 P.E.Siegbahn, and M.R.Blomberg (2009).
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19463779 T.Egawa, H.J.Lee, R.B.Gennis, S.R.Yeh, and D.L.Rousseau (2009).
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19204012 T.Mogi (2009).
Over-expression and characterization of Bacillus subtilis heme O synthase.
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18509049 A.V.Pisliakov, P.K.Sharma, Z.T.Chu, M.Haranczyk, and A.Warshel (2008).
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase.
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High tolerance for ionizable residues in the hydrophobic interior of proteins.
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18459161 D.Horn, and A.Barrientos (2008).
Mitochondrial copper metabolism and delivery to cytochrome c oxidase.
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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.
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18664577 E.A.Gorbikova, I.Belevich, M.Wikström, and M.I.Verkhovsky (2008).
The proton donor for O-O bond scission by cytochrome c oxidase.
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18798008 F.M.Ho (2008).
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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.
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18632561 J.P.Collman, A.Dey, R.A.Decreau, Y.Yang, A.Hosseini, E.I.Solomon, and T.A.Eberspacher (2008).
Interaction of nitric oxide with a functional model of cytochrome c oxidase.
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18956030 J.P.Collman, and R.A.Decréau (2008).
Functional biomimetic models for the active site in the respiratory enzyme cytochrome c oxidase.
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18155154 J.Xu, and G.A.Voth (2008).
Redox-coupled proton pumping in cytochrome c oxidase: further insights from computer simulation.
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18830692 M.A.Sharpe, and S.Ferguson-Miller (2008).
A chemically explicit model for the mechanism of proton pumping in heme-copper oxidases.
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18294138 M.S.Muntyan, and D.A.Bloch (2008).
Study of redox potential in cytochrome c covalently bound to terminal oxidase of alkaliphilic Bacillus pseudofirmus FTU.
  Biochemistry (Mosc), 73, 107-111.  
18771294 M.S.Rogers, R.Hurtado-Guerrero, S.J.Firbank, M.A.Halcrow, D.M.Dooley, S.E.Phillips, P.F.Knowles, and M.J.McPherson (2008).
Cross-link formation of the cysteine 228-tyrosine 272 catalytic cofactor of galactose oxidase does not require dioxygen.
  Biochemistry, 47, 10428-10439.
PDB codes: 2vz1 2vz3
18729107 N.Yeung, and Y.Lu (2008).
One heme, diverse functions: using biosynthetic myoglobin models to gain insights into heme-copper oxidases and nitric oxide reductases.
  Chem Biodivers, 5, 1437-1448.  
18824464 S.E.Hart, C.J.Howe, K.Mizuguchi, and J.Fernandez-Recio (2008).
Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum.
  Protein Eng Des Sel, 21, 689-698.  
18294124 V.B.Borisov (2008).
Interaction of bd-type quinol oxidase from Escherichia coli and carbon monoxide: heme d binds CO with high affinity.
  Biochemistry (Mosc), 73, 14-22.  
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, 0, 2197-2206.  
17895387 J.Treuffet, K.J.Kubarych, J.C.Lambry, E.Pilet, J.B.Masson, J.L.Martin, M.H.Vos, M.Joffre, and A.Alexandrou (2007).
Direct observation of ligand transfer and bond formation in cytochrome c oxidase by using mid-infrared chirped-pulse upconversion.
  Proc Natl Acad Sci U S A, 104, 15705-15710.  
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
17668091 K.N.White, I.Sen, I.Szundi, Y.R.Landaverry, L.E.Bria, J.P.Konopelski, M.M.Olmstead, and O.Einarsdóttir (2007).
Synthesis and structural characterization of cross-linked histidine-phenol Cu(ii) complexes as cytochrome c oxidase active site models.
  Chem Commun (Camb), 0, 3252-3254.  
17360500 K.Shimokata, Y.Katayama, H.Murayama, M.Suematsu, T.Tsukihara, K.Muramoto, H.Aoyama, S.Yoshikawa, and H.Shimada (2007).
The proton pumping pathway of bovine heart cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 104, 4200-4205.  
17350588 M.H.Olsson, P.E.Siegbahn, M.R.Blomberg, and A.Warshel (2007).
Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives.
  Biochim Biophys Acta, 1767, 244-260.  
18021062 P.Nicholls (2007).
The oxygenase-peroxidase theory of Bach and Chodat and its modern equivalents: change and permanence in scientific thinking as shown by our understanding of the roles of water, peroxide, and oxygen in the functioning of redox enzymes.
  Biochemistry (Mosc), 72, 1039-1046.  
18021063 P.R.Rich, and M.Iwaki (2007).
A comparison of catalytic site intermediates of cytochrome c oxidase and peroxidases.
  Biochemistry (Mosc), 72, 1047-1055.  
17277769 P.Syntichaki, K.Troulinaki, and N.Tavernarakis (2007).
eIF4E function in somatic cells modulates ageing in Caenorhabditis elegans.
  Nature, 445, 922-926.  
17375955 R.A.Decréau, J.P.Collman, Y.Yang, Y.Yan, and N.K.Devaraj (2007).
Syntheses of hemoprotein models that can be covalently attached onto electrode surfaces by click chemistry.
  J Org Chem, 72, 2794-2802.  
17997553 T.Hayashi, I.J.Lin, Y.Chen, J.A.Fee, and P.Moënne-Loccoz (2007).
Fourier transform infrared characterization of a CuB-nitrosyl complex in cytochrome ba3 from Thermus thermophilus: relevance to NO reductase activity in heme-copper terminal oxidases.
  J Am Chem Soc, 129, 14952-14958.  
17534481 X.Liang, D.J.Campopiano, and P.J.Sadler (2007).
Metals in membranes.
  Chem Soc Rev, 36, 968-992.  
17955155 Z.O.Wang, and D.D.Pollock (2007).
Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context.
  J Mol Evol, 65, 485-495.  
16477525 A.C.Dalziel, C.D.Moyes, E.Fredriksson, and S.C.Lougheed (2006).
Molecular evolution of cytochrome c oxidase in high-performance fish (teleostei: Scombroidei).
  J Mol Evol, 62, 319-331.  
16761090 D.M.Popovic, and A.A.Stuchebrukhov (2006).
Two conformational states of Glu242 and pKas in bovine cytochrome c oxidase.
  Photochem Photobiol Sci, 5, 611-620.  
16804678 H.Li, J.Igarashi, J.Jamal, W.Yang, and T.L.Poulos (2006).
Structural studies of constitutive nitric oxide synthases with diatomic ligands bound.
  J Biol Inorg Chem, 11, 753-768.
PDB codes: 2g6h 2g6i 2g6j 2g6k 2g6l 2g6m 2g6n 2g6o
16598262 I.Belevich, M.I.Verkhovsky, and M.Wikström (2006).
Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase.
  Nature, 440, 829-832.  
16791638 I.Bento, M.A.Carrondo, and P.F.Lindley (2006).
Reduction of dioxygen by enzymes containing copper.
  J Biol Inorg Chem, 11, 539-547.  
16789843 J.S.Winterle, and O.Einarsdóttir (2006).
Photoreactions of cytochrome C oxidase.
  Photochem Photobiol, 82, 711-719.  
17050688 L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, and S.Ferguson-Miller (2006).
Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 103, 16117-16122.
PDB code: 2gsm
17023543 L.S.Busenlehner, L.Salomonsson, P.Brzezinski, and R.N.Armstrong (2006).
Mapping protein dynamics in catalytic intermediates of the redox-driven proton pump cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 103, 15398-15403.  
16614069 M.H.Olsson, and A.Warshel (2006).
Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 103, 6500-6505.  
16788913 M.R.Blomberg, and P.E.Siegbahn (2006).
Quantum chemistry applied to the mechanisms of transition metal containing enzymes -- cytochrome c oxidase, a particularly challenging case.
  J Comput Chem, 27, 1373-1384.  
16352525 M.Seigneuret (2006).
Complete predicted three-dimensional structure of the facilitator transmembrane protein and hepatitis C virus receptor CD81: conserved and variable structural domains in the tetraspanin superfamily.
  Biophys J, 90, 212-227.
PDB code: 2avz
16728506 M.W.Bowler, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2006).
How azide inhibits ATP hydrolysis by the F-ATPases.
  Proc Natl Acad Sci U S A, 103, 8646-8649.
PDB code: 2ck3
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.  
16820845 R.P.Pesavento, D.A.Pratt, J.Jeffers, and W.A.van der Donk (2006).
Model studies of the Cu(B) site of cytochrome c oxidase utilizing a Zn(II) complex containing an imidazole-phenol cross-linked ligand.
  Dalton Trans, 0, 3326-3337.  
16373477 R.Schwartz, and J.King (2006).
Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure.
  Protein Sci, 15, 102-112.  
16983380 S.J.Lippard (2006).
The inorganic side of chemical biology.
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