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PDBsum entry 2dyr

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2dyr
Jmol
Contents
Protein chains
514 a.a. *
227 a.a. *
259 a.a. *
144 a.a. *
105 a.a. *
98 a.a. *
84 a.a. *
79 a.a. *
73 a.a. *
58 a.a. *
49 a.a. *
46 a.a. *
43 a.a. *
Ligands
HEA ×4
PGV ×8
CUA ×2
TGL ×6
PSC ×2
CHD ×8
DMU ×4
UNX ×2
PEK ×6
CDL ×4
Metals
_ZN ×2
_CU ×2
_MG ×2
_NA ×2
Waters ×2003
* Residue conservation analysis
PDB id:
2dyr
Name: Oxidoreductase
Title: Bovine heart cytochromE C oxidase at the fully oxidized stat
Structure: CytochromE C oxidase subunit 1. Chain: a, n. Synonym: cytochromE C oxidase polypeptide i. CytochromE C oxidase subunit 2. Chain: b, o. Synonym: cytochromE C oxidase polypeptide ii. CytochromE C oxidase subunit 3. Chain: c, p. Synonym: cytochromE C oxidase polypeptide iii.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Tissue: heart. Tissue: heart
Resolution:
1.80Å     R-factor:   0.202     R-free:   0.227
Authors: K.Shinzawa-Itoh,H.Aoyama,K.Muramoto,T.Kurauchi,T.Mizushima, E.Yamashita,T.Tsukihara,S.Yoshikawa
Key ref:
K.Shinzawa-Itoh et al. (2007). Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase. EMBO J, 26, 1713-1725. PubMed id: 17332748 DOI: 10.1038/sj.emboj.7601618
Date:
16-Sep-06     Release date:   03-Apr-07    
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.
259 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.
105 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.
79 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.
58 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.
46 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 4 residue positions (black crosses)

 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 50.60% 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   10 terms 
  Biological process     oxidation-reduction process   8 terms 
  Biochemical function     electron carrier activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1038/sj.emboj.7601618 EMBO J 26:1713-1725 (2007)
PubMed id: 17332748  
 
 
Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase.
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, S.Yoshikawa.
 
  ABSTRACT  
 
All 13 lipids, including two cardiolipins, one phosphatidylcholine, three phosphatidylethanolamines, four phosphatidylglycerols and three triglycerides, were identified in a crystalline bovine heart cytochrome c oxidase (CcO) preparation. The chain lengths and unsaturated bond positions of the fatty acid moieties determined by mass spectrometry suggest that each lipid head group identifies its specific binding site within CcOs. The X-ray structure demonstrates that the flexibility of the fatty acid tails facilitates their effective space-filling functions and that the four phospholipids stabilize the CcO dimer. Binding of dicyclohexylcarbodiimide to the O(2) transfer pathway of CcO causes two palmitate tails of phosphatidylglycerols to block the pathway, suggesting that the palmitates control the O(2) transfer process.The phosphatidylglycerol with vaccenate (cis-Delta(11)-octadecenoate) was found in CcOs of bovine and Paracoccus denitrificans, the ancestor of mitochondrion, indicating that the vaccenate is conserved in bovine CcO in spite of the abundance of oleate (cis-Delta(9)-octadecenoate). The X-ray structure indicates that the protein moiety selects cis-vaccenate near the O(2) transfer pathway against trans-vaccenate. These results suggest that vaccenate plays a critical role in the O(2) transfer mechanism.
 
  Selected figure(s)  
 
Figure 6.
Figure 6 CL1 bridging the two monomers. (A) The atomic model of CL1 in stereo-view. The amino acids of the same monomer (A molecule) as the one to which CL1 belongs and those of the other monomer (B molecule) are shown in green and dark blue, respectively. (B) A schematic representation of the hydrophobic interactions and hydrogen bonding interactions of CL1. The shadowed circles represent sites participating in hydrophobic interactions and the open circles indicate sites participating in hydrogen bonds. The green and dark blue colors denote the different monomers as defined in (A).
Figure 7.
Figure 7 The conformational diversity of the hydrophobic tails of lipids in bovine heart CcO. The stick models of the lipids are superimposed by fixing the C-2 carbon of the glycerol frame and by fitting each glycerol moiety to the X-ray structure of 1,2-dilaurroyl-DL-phosphatidylethanolamine (inset) by the least squares method.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 1713-1725) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21220505 C.Osman, D.R.Voelker, and T.Langer (2011).
Making heads or tails of phospholipids in mitochondria.
  J Cell Biol, 192, 7.  
21518899 R.Arias-Cartin, S.Grimaldi, J.Pommier, P.Lanciano, C.Schaefer, P.Arnoux, G.Giordano, B.Guigliarelli, and A.Magalon (2011).
Cardiolipin-based respiratory complex activation in bacteria.
  Proc Natl Acad Sci U S A, 108, 7781-7786.  
20657548 C.Potting, C.Wilmes, T.Engmann, C.Osman, and T.Langer (2010).
Regulation of mitochondrial phospholipids by Ups1/PRELI-like proteins depends on proteolysis and Mdm35.
  EMBO J, 29, 2888-2898.  
21314620 G.E.Bronnikov, T.P.Kulagina, and A.V.Aripovsky (2010).
Dietary supplementation of old rats with hydrogenated peanut oil restores activities of mitochondrial respiratory complexes in skeletal muscles.
  Biochemistry (Mosc), 75, 1491-1497.  
20544074 J.Gubbens, and A.I.de Kroon (2010).
Proteome-wide detection of phospholipid-protein interactions in mitochondria by photocrosslinking and click chemistry.
  Mol Biosyst, 6, 1751-1759.  
20809990 J.V.Møller, C.Olesen, A.M.Winther, and P.Nissen (2010).
The sarcoplasmic Ca2+-ATPase: design of a perfect chemi-osmotic pump.
  Q Rev Biophys, 43, 501-566.  
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
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.  
20696931 M.Bogdanov, P.Heacock, Z.Guan, and W.Dowhan (2010).
Plasticity of lipid-protein interactions in the function and topogenesis of the membrane protein lactose permease from Escherichia coli.
  Proc Natl Acad Sci U S A, 107, 15057-15062.  
20373004 Y.Katayama, K.Shimokata, M.Suematsu, T.Ogura, T.Tsukihara, S.Yoshikawa, and H.Shimada (2010).
Cell-free synthesis of cytochrome c oxidase, a multicomponent membrane protein.
  J Bioenerg Biomembr, 42, 235-240.  
20396396 Y.Yoshioka, and M.Mitani (2010).
B3LYP study on reduction mechanisms from O2 to H2O at the catalytic sites of fully reduced and mixed-valence bovine cytochrome c oxidases.
  Bioinorg Chem Appl, (), 182804.  
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
19371718 E.Mileykovskaya, and W.Dowhan (2009).
Cardiolipin membrane domains in prokaryotes and eukaryotes.
  Biochim Biophys Acta, 1788, 2084-2091.  
  19570033 M.A.Kiebish, X.Han, H.Cheng, and T.N.Seyfried (2009).
In vitro growth environment produces lipidomic and electron transport chain abnormalities in mitochondria from non-tumorigenic astrocytes and brain tumours.
  ASN Neuro, 1, 0.  
19413994 M.Schlame, and M.Ren (2009).
The role of cardiolipin in the structural organization of mitochondrial membranes.
  Biochim Biophys Acta, 1788, 2080-2083.  
19656950 P.J.Rijken, R.H.Houtkooper, H.Akbari, J.F.Brouwers, M.C.Koorengevel, B.de Kruijff, M.Frentzen, F.M.Vaz, and A.I.de Kroon (2009).
Cardiolipin molecular species with shorter acyl chains accumulate in Saccharomyces cerevisiae mutants lacking the acyl coenzyme A-binding protein Acb1p: new insights into acyl chain remodeling of cardiolipin.
  J Biol Chem, 284, 27609-27619.  
19254571 R.Acin-Perez, E.Salazar, M.Kamenetsky, J.Buck, L.R.Levin, and G.Manfredi (2009).
Cyclic AMP produced inside mitochondria regulates oxidative phosphorylation.
  Cell Metab, 9, 265-276.  
19422785 S.M.Claypool (2009).
Cardiolipin, a critical determinant of mitochondrial carrier protein assembly and function.
  Biochim Biophys Acta, 1788, 2059-2068.  
19035631 G.F.Schneider, B.F.Shaw, A.Lee, E.Carillho, and G.M.Whitesides (2008).
Pathway for unfolding of ubiquitin in sodium dodecyl sulfate, studied by capillary electrophoresis.
  J Am Chem Soc, 130, 17384-17393.  
18759498 L.Qin, D.A.Mills, L.Buhrow, C.Hiser, and S.Ferguson-Miller (2008).
A conserved steroid binding site in cytochrome C oxidase.
  Biochemistry, 47, 9931-9933.
PDB code: 3dtu
18373617 M.A.Kiebish, X.Han, H.Cheng, A.Lunceford, C.F.Clarke, H.Moon, J.H.Chuang, and T.N.Seyfried (2008).
Lipidomic analysis and electron transport chain activities in C57BL/6J mouse brain mitochondria.
  J Neurochem, 106, 299-312.  
18560917 M.A.Kiebish, X.Han, H.Cheng, J.H.Chuang, and T.N.Seyfried (2008).
Brain mitochondrial lipid abnormalities in mice susceptible to spontaneous gliomas.
  Lipids, 43, 951-959.  
18703489 M.A.Kiebish, X.Han, H.Cheng, J.H.Chuang, and T.N.Seyfried (2008).
Cardiolipin and electron transport chain abnormalities in mouse brain tumor mitochondria: lipidomic evidence supporting the Warburg theory of cancer.
  J Lipid Res, 49, 2545-2556.  
  18751913 M.Bogdanov, E.Mileykovskaya, and W.Dowhan (2008).
Lipids in the assembly of membrane proteins and organization of protein supercomplexes: implications for lipid-linked disorders.
  Subcell Biochem, 49, 197-239.  
18077827 M.Schlame (2008).
Cardiolipin synthesis for the assembly of bacterial and mitochondrial membranes.
  J Lipid Res, 49, 1607-1620.  
18975062 P.Brzezinski, and R.B.Gennis (2008).
Cytochrome c oxidase: exciting progress and remaining mysteries.
  J Bioenerg Biomembr, 40, 521-531.  
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.  
18541608 S.Helling, S.Vogt, A.Rhiel, R.Ramzan, L.Wen, K.Marcus, and B.Kadenbach (2008).
Phosphorylation and kinetics of mammalian cytochrome c oxidase.
  Mol Cell Proteomics, 7, 1714-1724.  
17923475 D.J.Mancuso, H.F.Sims, X.Han, C.M.Jenkins, S.P.Guan, K.Yang, S.H.Moon, T.Pietka, N.A.Abumrad, P.H.Schlesinger, and R.W.Gross (2007).
Genetic ablation of calcium-independent phospholipase A2gamma leads to alterations in mitochondrial lipid metabolism and function resulting in a deficient mitochondrial bioenergetic phenotype.
  J Biol Chem, 282, 34611-34622.  
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.  
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.