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PDBsum entry 1fft

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1fft
Jmol
Contents
Protein chains
501 a.a. *
257 a.a. *
185 a.a. *
109 a.a. *
Ligands
HEM ×2
HEO ×2
Metals
_CU ×2
* Residue conservation analysis
PDB id:
1fft
Name: Oxidoreductase
Title: The structure of ubiquinol oxidase from escherichia coli
Structure: Ubiquinol oxidase. Chain: a, f. Engineered: yes. Ubiquinol oxidase. Chain: b, g. Engineered: yes. Ubiquinol oxidase. Chain: c, h. Engineered: yes.
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
3.50Å     R-factor:   not given    
Authors: J.Abramson,S.Riistama,G.Larsson,A.Jasaitis,M.Svensson-Ek,A.P S.Iwata,M.Wikstrom
Key ref:
J.Abramson et al. (2000). The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site. Nat Struct Biol, 7, 910-917. PubMed id: 11017202 DOI: 10.1038/82824
Date:
26-Jul-00     Release date:   18-Oct-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0ABI8  (CYOB_ECOLI) -  Cytochrome bo(3) ubiquinol oxidase subunit 1
Seq:
Struc:
 
Seq:
Struc:
663 a.a.
501 a.a.
Protein chains
Pfam   ArchSchema ?
P0ABJ1  (CYOA_ECOLI) -  Cytochrome bo(3) ubiquinol oxidase subunit 2
Seq:
Struc:
315 a.a.
257 a.a.
Protein chains
Pfam   ArchSchema ?
P0ABJ3  (CYOC_ECOLI) -  Cytochrome bo(3) ubiquinol oxidase subunit 3
Seq:
Struc:
204 a.a.
185 a.a.
Protein chains
No UniProt id for this chain
Struc: 109 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, F: E.C.1.10.3.10  - Ubiquinol oxidase (H(+)-transporting).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 ubiquinol + O2 + n H+(Side 1) = 2 ubiquinone + 2 H2O + n H+(Side 2)
2 × ubiquinol
+ O(2)
+ n H(+)(Side 1)
= 2 × ubiquinone
+ 2 × H(2)O
+ n H(+)(Side 2)
      Cofactor: Cu cation; Heme
Cu cation
Heme
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   6 terms 
  Biological process     oxidation-reduction process   8 terms 
  Biochemical function     electron carrier activity     15 terms  

 

 
    reference    
 
 
DOI no: 10.1038/82824 Nat Struct Biol 7:910-917 (2000)
PubMed id: 11017202  
 
 
The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site.
J.Abramson, S.Riistama, G.Larsson, A.Jasaitis, M.Svensson-Ek, L.Laakkonen, A.Puustinen, S.Iwata, M.Wikström.
 
  ABSTRACT  
 
Cell respiration is catalyzed by the heme-copper oxidase superfamily of enzymes, which comprises cytochrome c and ubiquinol oxidases. These membrane proteins utilize different electron donors through dissimilar access mechanisms. We report here the first structure of a ubiquinol oxidase, cytochrome bo3, from Escherichia coli. The overall structure of the enzyme is similar to those of cytochrome c oxidases; however, the membrane-spanning region of subunit I contains a cluster of polar residues exposed to the interior of the lipid bilayer that is not present in the cytochrome c oxidase. Mutagenesis studies on these residues strongly suggest that this region forms a quinone binding site. A sequence comparison of this region with known quinone binding sites in other membrane proteins shows remarkable similarities. In light of these findings we suggest specific roles for these polar residues in electron and proton transfer in ubiquinol oxidase.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Schematic representation of electron and proton transfer in ubiquinol oxidase.
Figure 6.
Figure 6. A possible ubiquinone binding site in ubiquinol oxidase. a, View of subunit I parallel to the membrane with modeled ubiquinone-2. Helices I, II and III of subunit I are colored blue, and ubiquinone-2 and heme b are colored black and red, respectively. The polar residues (Arg 71, Asp 75, His 98 and Glu 101) forming the ubiquinone binding site are shown in green. b, View of subunit I along the membrane normal from the periplasmic side with the modeled ubiquinone-2. A possible electron path from the ubiquinone to the binuclear center (heme o[3] and Cu[B]) via heme b is shown by a dotted line. The residues in the path (Ile 102, Met 79, Phe 103 and His ligands for hemes) are shown in pink. c,d, Detailed views of the ubiquinone binding site parallel to the membrane (c) and along the membrane normal from the periplasmic side (d).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 910-917) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22266822 Y.Matsumoto, T.Tosha, A.V.Pisliakov, T.Hino, H.Sugimoto, S.Nagano, Y.Sugita, and Y.Shiro (2012).
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PDB codes: 3ayf 3ayg
21453708 S.Wu, S.Liu, C.H.Davis, D.W.Stafford, J.D.Kulman, and L.G.Pedersen (2011).
A hetero-dimer model for concerted action of vitamin K carboxylase and vitamin K reductase in vitamin K cycle.
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20370613 A.V.Kalinovich, N.V.Azarkina, T.V.Vygodina, T.Soulimane, and A.A.Konstantinov (2010).
Peculiarities of cyanide binding to the ba3-type cytochrome oxidase from the thermophilic bacterium Thermus thermophilus.
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21110891 H.C.Tseng, C.L.Harwell, C.H.Martin, and K.L.Prather (2010).
Biosynthesis of chiral 3-hydroxyvalerate from single propionate-unrelated carbon sources in metabolically engineered E. coli.
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20544970 L.J.Smith, A.Kahraman, and J.M.Thornton (2010).
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20576851 S.Buschmann, E.Warkentin, H.Xie, J.D.Langer, U.Ermler, and H.Michel (2010).
The structure of cbb3 cytochrome oxidase provides insights into proton pumping.
  Science, 329, 327-330.
PDB code: 3mk7
20204450 S.J.Facey, and A.Kuhn (2010).
Biogenesis of bacterial inner-membrane proteins.
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20623242 V.S.Oganesyan, G.F.White, S.Field, S.Marritt, R.B.Gennis, L.L.Yap, and A.J.Thomson (2010).
Nitroxide spin labels as EPR reporters of the relaxation and magnetic properties of the heme-copper site in cytochrome bo3, E. coli.
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19218360 K.Kobayashi, S.Tagawa, and T.Mogi (2009).
Intramolecular electron transfer processes in Cu(B)-deficient cytochrome bo studied by pulse radiolysis.
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Electron transfer processes in subunit I mutants of cytochrome bo quinol oxidase in Escherichia coli.
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19719482 M.S.Albury, C.Elliott, and A.L.Moore (2009).
Towards a structural elucidation of the alternative oxidase in plants.
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19174546 T.Mogi (2009).
Effects of replacement of low-spin haem b by haem O on Escherichia coli cytochromes bo and bd quinol oxidases.
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19204012 T.Mogi (2009).
Over-expression and characterization of Bacillus subtilis heme O synthase.
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A lipidic-sponge phase screen for membrane protein crystallization.
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The cbb3 oxidases are an ancient innovation of the domain bacteria.
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Amino acid residues interacting with both the bound quinone and coenzyme, pyrroloquinoline quinone, in Escherichia coli membrane-bound glucose dehydrogenase.
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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.  
18983149 M.T.Lin, R.I.Samoilova, R.B.Gennis, and S.A.Dikanov (2008).
Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli.
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18155041 N.Celebi, R.E.Dalbey, and J.Yuan (2008).
Mechanism and hydrophobic forces driving membrane protein insertion of subunit II of cytochrome bo 3 oxidase.
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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.
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18975062 P.Brzezinski, and R.B.Gennis (2008).
Cytochrome c oxidase: exciting progress and remaining mysteries.
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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.
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18953727 S.Gupta, and S.Mazumdar (2008).
Inhibition of bacterial oxidases by formamide and analogs.
  Biol Chem, 389, 599-607.  
18294124 V.B.Borisov (2008).
Interaction of bd-type quinol oxidase from Escherichia coli and carbon monoxide: heme d binds CO with high affinity.
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18430799 V.R.Kaila, M.I.Verkhovsky, G.Hummer, and M.Wikström (2008).
Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase.
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18087041 A.Jasaitis, M.P.Johansson, M.Wikström, M.H.Vos, and M.I.Verkhovsky (2007).
Nanosecond electron tunneling between the hemes in cytochrome bo3.
  Proc Natl Acad Sci U S A, 104, 20811-20814.  
17130127 B.J.Jepson, S.Mohan, T.A.Clarke, A.J.Gates, J.A.Cole, C.S.Butler, J.N.Butt, A.M.Hemmings, and D.J.Richardson (2007).
Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli.
  J Biol Chem, 282, 6425-6437.
PDB code: 2nya
17288564 H.Yamada, E.Takashima, and K.Konishi (2007).
Molecular characterization of the membrane-bound quinol peroxidase functionally connected to the respiratory chain.
  FEBS J, 274, 853-866.  
17977822 J.Torres-Bacete, E.Nakamaru-Ogiso, A.Matsuno-Yagi, and T.Yagi (2007).
Characterization of the NuoM (ND4) Subunit in Escherichia coli NDH-1: CONSERVED CHARGED RESIDUES ESSENTIAL FOR ENERGY-COUPLED ACTIVITIES.
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17267395 L.L.Yap, R.I.Samoilova, R.B.Gennis, and S.A.Dikanov (2007).
Characterization of mutants that change the hydrogen bonding of the semiquinone radical at the QH site of the cytochrome bo3 from Escherichia coli.
  J Biol Chem, 282, 8777-8785.  
17534481 X.Liang, D.J.Campopiano, and P.J.Sadler (2007).
Metals in membranes.
  Chem Soc Rev, 36, 968-992.  
16513637 D.J.du Plessis, N.Nouwen, and A.J.Driessen (2006).
Subunit a of cytochrome o oxidase requires both YidC and SecYEG for membrane insertion.
  J Biol Chem, 281, 12248-12252.  
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.  
16481320 E.van Bloois, G.J.Haan, J.W.de Gier, B.Oudega, and J.Luirink (2006).
Distinct requirements for translocation of the N-tail and C-tail of the Escherichia coli inner membrane protein CyoA.
  J Biol Chem, 281, 10002-10009.  
16964530 H.L.Frericks, D.H.Zhou, L.L.Yap, R.B.Gennis, and C.M.Rienstra (2006).
Magic-angle spinning solid-state NMR of a 144 kDa membrane protein complex: E. coli cytochrome bo3 oxidase.
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16402141 J.P.Collman, M.Kaplun, and R.A.Decréau (2006).
Metal corroles as electrocatalysts for oxygen reduction.
  Dalton Trans, (), 554-559.  
16789843 J.S.Winterle, and O.Einarsdóttir (2006).
Photoreactions of cytochrome C oxidase.
  Photochem Photobiol, 82, 711-719.  
17050691 J.Zhang, F.E.Frerman, and J.J.Kim (2006).
Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
  Proc Natl Acad Sci U S A, 103, 16212-16217.
PDB codes: 2gmh 2gmj
16624801 L.L.Yap, R.I.Samoilova, R.B.Gennis, and S.A.Dikanov (2006).
Characterization of the exchangeable protons in the immediate vicinity of the semiquinone radical at the QH site of the cytochrome bo3 from Escherichia coli.
  J Biol Chem, 281, 16879-16887.  
17203431 L.Laakkonen, R.W.Jobson, and V.A.Albert (2006).
A new model for the evolution of carnivory in the bladderwort plant (utricularia): adaptive changes in cytochrome C oxidase (COX) provide respiratory power.
  Plant Biol (Stuttg), 8, 758-764.  
17139260 M.L.Rodrigues, T.F.Oliveira, I.A.Pereira, and M.Archer (2006).
X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination.
  EMBO J, 25, 5951-5960.
PDB code: 2j7a
16842995 P.Brzezinski, and P.Adelroth (2006).
Design principles of proton-pumping haem-copper oxidases.
  Curr Opin Struct Biol, 16, 465-472.  
16373477 R.Schwartz, and J.King (2006).
Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure.
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16864586 S.M.Southall, J.J.Doel, D.J.Richardson, and A.Oubrie (2006).
Soluble aldose sugar dehydrogenase from Escherichia coli: a highly exposed active site conferring broad substrate specificity.
  J Biol Chem, 281, 30650-30659.
PDB code: 2g8s
16299377 Y.Matsumoto, M.Murai, D.Fujita, K.Sakamoto, H.Miyoshi, M.Yoshida, and T.Mogi (2006).
Mass spectrometric analysis of the ubiquinol-binding site in cytochrome bd from Escherichia coli.
  J Biol Chem, 281, 1905-1912.  
16319876 D.M.Engelman (2005).
Membranes are more mosaic than fluid.
  Nature, 438, 578-580.  
16040612 H.Kandori, H.Nakamura, Y.Yamazaki, and T.Mogi (2005).
Redox-induced protein structural changes in cytochrome bo revealed by Fourier transform infrared spectroscopy and [13C]Tyr labeling.
  J Biol Chem, 280, 32821-32826.  
15654878 O.M.Richter, K.L.Dürr, A.Kannt, B.Ludwig, F.M.Scandurra, A.Giuffrè, P.Sarti, and P.Hellwig (2005).
Probing the access of protons to the K pathway in the Paracoccus denitrificans cytochrome c oxidase.
  FEBS J, 272, 404-412.  
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.  
16234916 R.L.Lieberman, and A.C.Rosenzweig (2005).
The quest for the particulate methane monooxygenase active site.
  Dalton Trans, (), 3390-3396.  
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.  
15377522 B.L.Victor, A.M.Baptista, and C.M.Soares (2004).
Theoretical identification of proton channels in the quinol oxidase aa3 from Acidianus ambivalens.
  Biophys J, 87, 4316-4325.  
14766756 M.Fabian, D.Jancura, and G.Palmer (2004).
Two sites of interaction of anions with cytochrome a in oxidized bovine cytochrome c oxidase.
  J Biol Chem, 279, 16170-16177.  
14672950 M.Paumann, B.Lubura, G.Regelsberger, M.Feichtinger, G.Köllensberger, C.Jakopitsch, P.G.Furtmüller, G.A.Peschek, and C.Obinger (2004).
Soluble CuA domain of cyanobacterial cytochrome c oxidase.
  J Biol Chem, 279, 10293-10303.  
15236746 P.Brzezinski (2004).
Redox-driven membrane-bound proton pumps.
  Trends Biochem Sci, 29, 380-387.  
15364957 R.E.Dalbey, and A.Kuhn (2004).
YidC family members are involved in the membrane insertion, lateral integration, folding, and assembly of membrane proteins.
  J Cell Biol, 166, 769-774.  
15465820 T.Uchida, T.Mogi, H.Nakamura, and T.Kitagawa (2004).
Role of Tyr-288 at the dioxygen reduction site of cytochrome bo studied by stable isotope labeling and resonance raman spectroscopy.
  J Biol Chem, 279, 53613-53620.  
12958362 A.Changela, K.Chen, Y.Xue, J.Holschen, C.E.Outten, T.V.O'Halloran, and A.Mondragón (2003).
Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR.
  Science, 301, 1383-1387.
PDB codes: 1q05 1q06 1q07 1q08 1q09 1q0a
14676323 A.Namslauer, A.S.Pawate, R.B.Gennis, and P.Brzezinski (2003).
Redox-coupled proton translocation in biological systems: proton shuttling in cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 100, 15543-15547.  
12446663 A.Niebisch, and M.Bott (2003).
Purification of a cytochrome bc-aa3 supercomplex with quinol oxidase activity from Corynebacterium glutamicum. Identification of a fourth subunity of cytochrome aa3 oxidase and mutational analysis of diheme cytochrome c1.
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12668481 E.Ching, R.B.Gennis, and R.W.Larsen (2003).
Kinetics of intramolecular electron transfer in cytochrome bo3 from Escherichia coli.
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14527321 G.Cecchini (2003).
Function and structure of complex II of the respiratory chain.
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12614840 P.Sarti, A.Giuffrè, M.C.Barone, E.Forte, D.Mastronicola, and M.Brunori (2003).
Nitric oxide and cytochrome oxidase: reaction mechanisms from the enzyme to the cell.
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12799376 S.de Vries, M.J.Strampraad, S.Lu, P.Moënne-Loccoz, and I.Schröder (2003).
Purification and characterization of the MQH2:NO oxidoreductase from the hyperthermophilic archaeon Pyrobaculum aerophilum.
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11959503 B.Byrne, and S.Iwata (2002).
Membrane protein complexes.
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12027903 C.Ludovici, R.Fröhlich, K.Vogtt, B.Mamat, and M.Lübben (2002).
Caged O(2). Reaction of cytochrome bo(3) oxidase with photochemically released dioxygen from a cobalt peroxo complex.
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11864982 J.I.Oh, and S.Kaplan (2002).
Oxygen adaptation. The role of the CcoQ subunit of the cbb3 cytochrome c oxidase of Rhodobacter sphaeroides 2.4.1.
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12097331 K.Koutsoupakis, S.Stavrakis, E.Pinakoulaki, T.Soulimane, and C.Varotsis (2002).
Observation of the equilibrium CuB-CO complex and functional implications of the transient heme a3 propionates in cytochrome ba3-CO from Thermus thermophilus. Fourier transform infrared (FTIR) and time-resolved step-scan FTIR studies.
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Vitreoscilla hemoglobin binds to subunit I of cytochrome bo ubiquinol oxidases.
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Structure-function relationships in heme-proteins.
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12186553 P.Hellwig, T.Yano, T.Ohnishi, and R.B.Gennis (2002).
Identification of the residues involved in stabilization of the semiquinone radical in the high-affinity ubiquinone binding site in cytochrome bo(3) from Escherichia coli by site-directed mutagenesis and EPR spectroscopy.
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12070166 R.S.Pitcher, M.R.Cheesman, and N.J.Watmough (2002).
Molecular and spectroscopic analysis of the cytochrome cbb(3) oxidase from Pseudomonas stutzeri.
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11850430 T.M.Iverson, C.Luna-Chavez, L.R.Croal, G.Cecchini, and D.C.Rees (2002).
Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site.
  J Biol Chem, 277, 16124-16130.
PDB codes: 1kf6 1kfy 1l0v
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Structure of cytochrome c oxidase: a comparison of the bacterial and mitochondrial enzymes.
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11518705 K.Kobayashi, S.Tagawa, S.Daff, I.Sagami, and T.Shimizu (2001).
Rapid calmodulin-dependent interdomain electron transfer in neuronal nitric-oxide synthase measured by pulse radiolysis.
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11334784 M.M.Pereira, M.Santana, and M.Teixeira (2001).
A novel scenario for the evolution of haem-copper oxygen reductases.
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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.