PDBsum entry 1ehk

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
544 a.a. *
166 a.a. *
33 a.a. *
BNG ×3
Waters ×119
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of the aberrant ba3-cytochromE-C oxidase f thermus thermophilus
Structure: Ba3-type cytochromE-C oxidase. Chain: a. Fragment: subunit i. Ba3-type cytochromE-C oxidase. Chain: b. Fragment: subunit ii. Ba3-type cytochromE-C oxidase. Chain: c. Fragment: subunit iia.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Strain: hb8
Biol. unit: Trimer (from PQS)
2.40Å     R-factor:   0.222     R-free:   0.264
Authors: T.Soulimane,G.Buse,G.P.Bourenkov,H.D.Bartunik,R.Huber,M.E.Th
Key ref:
T.Soulimane et al. (2000). Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus. EMBO J, 19, 1766-1776. PubMed id: 10775261 DOI: 10.1093/emboj/19.8.1766
21-Feb-00     Release date:   22-Feb-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q5SJ79  (COX1_THET8) -  Cytochrome c oxidase subunit 1
562 a.a.
544 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ80  (COX2_THET8) -  Cytochrome c oxidase subunit 2
168 a.a.
166 a.a.
Protein chain
Pfam   ArchSchema ?
P82543  (COXA_THET8) -  Cytochrome c oxidase polypeptide 2A
34 a.a.
33 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C: 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 = HEM)
matches with 63.64% similarity
+ O(2)
+ 4 × H(+)
= 4 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Cu cation
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   7 terms 
  Biochemical function     electron carrier activity     7 terms  


DOI no: 10.1093/emboj/19.8.1766 EMBO J 19:1766-1776 (2000)
PubMed id: 10775261  
Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus.
T.Soulimane, G.Buse, G.P.Bourenkov, H.D.Bartunik, R.Huber, M.E.Than.
Cytochrome c oxidase is a respiratory enzyme catalysing the energy-conserving reduction of molecular oxygen to water. The crystal structure of the ba(3)-cytochrome c oxidase from Thermus thermophilus has been determined to 2.4 A resolution using multiple anomalous dispersion (MAD) phasing and led to the discovery of a novel subunit IIa. A structure-based sequence alignment of this phylogenetically very distant oxidase with the other structurally known cytochrome oxidases leads to the identification of sequence motifs and residues that seem to be indispensable for the function of the haem copper oxidases, e.g. a new electron transfer pathway leading directly from Cu(A) to Cu(B). Specific features of the ba(3)-oxidase include an extended oxygen input channel, which leads directly to the active site, the presence of only one oxygen atom (O(2-), OH(-) or H(2)O) as bridging ligand at the active site and the mainly hydrophobic character of the interactions that stabilize the electron transfer complex between this oxidase and its substrate cytochrome c. New aspects of the proton pumping mechanism could be identified.
  Selected figure(s)  
Figure 2.
Figure 2 Stereo representation of the binuclear centre haem a[s3] Cu[B] including the final 2F[obs] - F[calc] electron density map contoured at 1.0 (blue). Haem a[s3], the histidine ligands and the covalently linked Tyr237 are shown as stick models in orange and green, respectively. The covalent bond between Tyr237 and His233 is well defined in the electron density. The F[obs] - F[calc] difference electron density (contoured at 5.0 , green) between the haem a[s3] iron and Cu[B] (cyan) is of almost spherical shape and is best interpreted as one oxygen atom (O^2-, OH^- or H[2]O; purple), located equidistant between the two metal atoms. This figure was prepared with MAIN (Turk, 1992).
Figure 5.
Figure 5 Stereo representation of the electron transfer pathways in the ba[3]-cytochrome c oxidase from T.thermophilus. The haems b and a[s3] are shown in orange, the copper atoms in blue and the metal-ligating amino acid residues in green. The two arginine residues (Arg450 and Arg449) and Phe385, which are involved in the electron transfer from Cu[A] via haem b to the active site haem a[s3] Cu[B] are depicted in purple. The residues that form the newly postulated electron transfer pathway leading from Cu[A] to the aromatic ring system of Tyr136 and from there via a hydrogen bond and Trp229 to the Cu[B] ligand His238 are represented in cyan, including the corresponding distances. This figure was prepared with MAIN (Turk, 1992).
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 1766-1776) copyright 2000.  
  Figures were selected by an automated process.  

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
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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21107730 M.Oztürk, and N.J.Watmough (2011).
Mutagenesis of tyrosine residues within helix VII in subunit I of the cytochrome cbb (3) oxidase from Rhodobacter capsulatus.
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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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20622059 C.Werner, O.M.Richter, and B.Ludwig (2010).
A novel heme a insertion factor gene cotranscribes with the Thermus thermophilus cytochrome ba3 oxidase locus.
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20037139 D.Parul, G.Palmer, and M.Fabian (2010).
Ligand trapping by cytochrome c oxidase: implications for gating at the catalytic center.
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21097703 I.Szundi, C.Funatogawa, J.A.Fee, T.Soulimane, and O.Einarsdóttir (2010).
CO impedes superfast O2 binding in ba3 cytochrome oxidase from Thermus thermophilus.
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19826804 K.McLuskey, A.W.Roszak, Y.Zhu, and N.W.Isaacs (2010).
Crystal structures of all-alpha type membrane proteins.
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20192226 S.A.Siletsky, J.Zhu, R.B.Gennis, and A.A.Konstantinov (2010).
Partial steps of charge translocation in the nonpumping N139L mutant of Rhodobacter sphaeroides cytochrome c oxidase with a blocked D-channel.
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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
21109633 T.Hino, Y.Matsumoto, S.Nagano, H.Sugimoto, Y.Fukumori, T.Murata, S.Iwata, and Y.Shiro (2010).
Structural basis of biological N2O generation by bacterial nitric oxide reductase.
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PDB code: 3o0r
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.
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19438285 A.Offenbacher, K.N.White, I.Sen, A.G.Oliver, J.P.Konopelski, B.A.Barry, and O.Einarsdóttir (2009).
A spectroscopic investigation of a tridentate Cu-complex mimicking the tyrosine-histidine cross-link of 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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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
19156357 F.Cava, A.Hidalgo, and J.Berenguer (2009).
Thermus thermophilus as biological model.
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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.
  Proc Natl Acad Sci U S A, 106, 2165-2169.
PDB codes: 2zxw 3abl 3abm
19805275 H.Y.Chang, J.Hemp, Y.Chen, J.A.Fee, and R.B.Gennis (2009).
The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping.
  Proc Natl Acad Sci U S A, 106, 16169-16173.  
19862409 I.Radu, M.Schleeger, C.Bolwien, and J.Heberle (2009).
Time-resolved methods in biophysics. 10. Time-resolved FT-IR difference spectroscopy and the application to membrane proteins.
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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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19146411 L.A.Abriata, G.N.Ledesma, R.Pierattelli, and A.J.Vila (2009).
Electronic structure of the ground and excited states of the Cu(A) site by NMR spectroscopy.
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19191487 N.Xu, A.L.Campbell, D.R.Powell, J.Khandogin, and G.B.Richter-Addo (2009).
A stable hyponitrite-bridged iron porphyrin complex.
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19187032 T.Hayashi, M.T.Lin, K.Ganesan, Y.Chen, J.A.Fee, R.B.Gennis, and P.Moënne-Loccoz (2009).
Accommodation of two diatomic molecules in cytochrome bo: insights into NO reductase activity in terminal oxidases.
  Biochemistry, 48, 883-890.  
19204012 T.Mogi (2009).
Over-expression and characterization of Bacillus subtilis heme O synthase.
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19252222 V.Rauhamäki, D.A.Bloch, M.I.Verkhovsky, and M.Wikström (2009).
Active Site of Cytochrome cbb3.
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18766386 Y.El Khoury, and P.Hellwig (2009).
Infrared spectroscopic characterization of copper-polyhistidine from 1,800 to 50 cm(-1): model systems for copper coordination.
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18676644 A.F.Veríssimo, F.L.Sousa, A.M.Baptista, M.Teixeira, and M.M.Pereira (2008).
Thermodynamic redox behavior of the heme centers in A-type heme-copper oxygen reductases: comparison between the two subfamilies.
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18761683 F.Cava, O.Zafra, and J.Berenguer (2008).
A cytochrome c containing nitrate reductase plays a role in electron transport for denitrification in Thermus thermophilus without involvement of the bc respiratory complex.
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18065462 F.L.Sousa, A.F.Veríssimo, A.M.Baptista, T.Soulimane, M.Teixeira, and M.M.Pereira (2008).
Redox properties of Thermus thermophilus ba3: different electron-proton coupling in oxygen reductases?
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18752061 I.A.Smirnova, D.Zaslavsky, J.A.Fee, R.B.Gennis, and P.Brzezinski (2008).
Electron and proton transfer in the ba (3) oxidase from Thermus thermophilus.
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17949262 I.Belevich, and M.I.Verkhovsky (2008).
Molecular mechanism of proton translocation by cytochrome C oxidase.
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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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18614534 L.Piubelli, M.Pedotti, G.Molla, S.Feindler-Boeckh, S.Ghisla, M.S.Pilone, and L.Pollegioni (2008).
  J Biol Chem, 283, 24738-24747.  
18536726 M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, and S.Iwata (2008).
Molecular mechanism of energy conservation in polysulfide respiration.
  Nat Struct Mol Biol, 15, 730-737.
PDB codes: 2vpw 2vpx 2vpy 2vpz
18214976 la Cruz, F.C.Peterson, and B.F.Volkman (2008).
Solution structure of At3g28950 from Arabidopsis thaliana.
  Proteins, 71, 546-551.
PDB code: 2jqv
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.  
18975062 P.Brzezinski, and R.B.Gennis (2008).
Cytochrome c oxidase: exciting progress and remaining mysteries.
  J Bioenerg Biomembr, 40, 521-531.  
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.
  Proc Natl Acad Sci U S A, 105, 6255-6259.  
  18084085 B.Liu, V.M.Luna, Y.Chen, C.D.Stout, and J.A.Fee (2007).
An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1029-1034.
PDB codes: 2qpd 2qpe
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.  
17242410 J.D.Otero-Cruz, C.A.Báez-Pagán, I.M.Caraballo-González, and J.A.Lasalde-Dominicci (2007).
Tryptophan-scanning mutagenesis in the alphaM3 transmembrane domain of the muscle-type acetylcholine receptor. A spring model revealed.
  J Biol Chem, 282, 9162-9171.  
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), (), 3252-3254.  
17534533 P.Moënne-Loccoz (2007).
Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins.
  Nat Prod Rep, 24, 610-620.  
17549469 S.Bernad, N.Leygue, H.Korri-Youssoufi, and S.Lecomte (2007).
Kinetics of the electron transfer reaction of Cytochrome c (552) adsorbed on biomimetic electrode studied by time-resolved surface-enhanced resonance Raman spectroscopy and electrochemistry.
  Eur Biophys J, 36, 1039-1048.  
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.  
18021064 T.V.Vygodina, and A.A.Konstantinov (2007).
Peroxidase activity of mitochondrial cytochrome c oxidase.
  Biochemistry (Mosc), 72, 1056-1064.  
17534481 X.Liang, D.J.Campopiano, and P.J.Sadler (2007).
Metals in membranes.
  Chem Soc Rev, 36, 968-992.  
16704969 D.Jancura, M.Antalik, V.Berka, G.Palmer, and M.Fabian (2006).
Filling the catalytic site of cytochrome c oxidase with electrons. Reduced CuB facilitates internal electron transfer to heme a3.
  J Biol Chem, 281, 20003-20010.  
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.  
17046020 I.M.Moustafa, S.Foster, A.Y.Lyubimov, and A.Vrielink (2006).
Crystal structure of LAAO from Calloselasma rhodostoma with an L-phenylalanine substrate: insights into structure and mechanism.
  J Mol Biol, 364, 991.
PDB code: 2iid
17176062 J.Hemp, D.E.Robinson, K.B.Ganesan, T.J.Martinez, N.L.Kelleher, and R.B.Gennis (2006).
Evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases.
  Biochemistry, 45, 15405-15410.  
16789843 J.S.Winterle, and O.Einarsdóttir (2006).
Photoreactions of cytochrome C oxidase.
  Photochem Photobiol, 82, 711-719.  
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.  
16554303 L.Muresanu, P.Pristovsek, F.Löhr, O.Maneg, M.D.Mukrasch, H.Rüterjans, B.Ludwig, and C.Lücke (2006).
The electron transfer complex between cytochrome c552 and the CuA domain of the Thermus thermophilus ba3 oxidase. A combined NMR and computational approach.
  J Biol Chem, 281, 14503-14513.
PDB code: 2fwl
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.  
16842995 P.Brzezinski, and P.Adelroth (2006).
Design principles of proton-pumping haem-copper oxidases.
  Curr Opin Struct Biol, 16, 465-472.  
16365847 S.Bernad, T.Soulimane, Z.Mehkalif, and S.Lecomte (2006).
Characterization and redox properties of cytochrome c552 from Thermus thermophilus adsorbed on different self-assembled thiol monolayers, used to model the chemical environment of the redox partner.
  Biopolymers, 81, 407-418.  
15653739 B.Nie, J.Stutzman, and A.Xie (2005).
A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues.
  Biophys J, 88, 2833-2847.  
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.  
15735345 L.M.Hunsicker-Wang, R.L.Pacoma, Y.Chen, J.A.Fee, and C.D.Stout (2005).
A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus.
  Acta Crystallogr D Biol Crystallogr, 61, 340-343.
PDB code: 1xme
16306266 L.Salomonsson, K.Faxén, P.Adelroth, and P.Brzezinski (2005).
The timing of proton migration in membrane-reconstituted cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 102, 17624-17629.  
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.  
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.  
15041681 C.Koutsoupakis, T.Soulimane, and C.Varotsis (2004).
Probing the Q-proton pathway of ba3-cytochrome c oxidase by time-resolved Fourier transform infrared spectroscopy.
  Biophys J, 86, 2438-2444.  
15066990 E.Pinakoulaki, T.Ohta, T.Soulimane, T.Kitagawa, and C.Varotsis (2004).
Simultaneous resonance Raman detection of the heme a3-Fe-CO and CuB-CO species in CO-bound ba3-cytochrome c oxidase from Thermus thermophilus. Evidence for a charge transfer CuB-CO transition.
  J Biol Chem, 279, 22791-22794.  
15504726 H.Kumita, K.Matsuura, T.Hino, S.Takahashi, H.Hori, Y.Fukumori, I.Morishima, and Y.Shiro (2004).
NO reduction by nitric-oxide reductase from denitrifying bacterium Pseudomonas aeruginosa: characterization of reaction intermediates that appear in the single turnover cycle.
  J Biol Chem, 279, 55247-55254.  
15289603 L.Salomonsson, A.Lee, R.B.Gennis, and P.Brzezinski (2004).
A single-amino-acid lid renders a gas-tight compartment within a membrane-bound transporter.
  Proc Natl Acad Sci U S A, 101, 11617-11621.  
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.  
15465852 M.Gimpelev, L.R.Forrest, D.Murray, and B.Honig (2004).
Helical packing patterns in membrane and soluble proteins.
  Biophys J, 87, 4075-4086.  
15137098 M.Wolpert, O.Maneg, B.Ludwig, and P.Hellwig (2004).
Characterization of the CuA center in the cytochrome c oxidase from Thermus thermophilus for the spectral range 1800-500 cm-1 with a combined electrochemical and Fourier transform infrared spectroscopic setup.
  Biopolymers, 74, 73-76.  
15236746 P.Brzezinski (2004).
Redox-driven membrane-bound proton pumps.
  Trends Biochem Sci, 29, 380-387.  
15189883 S.Bernad, S.Oellerich, T.Soulimane, S.Noinville, M.H.Baron, M.Paternostre, and S.Lecomte (2004).
Interaction of horse heart and thermus thermophilus type c cytochromes with phospholipid vesicles and hydrophobic surfaces.
  Biophys J, 86, 3863-3872.  
14728676 S.Ghisla, and C.Thorpe (2004).
Acyl-CoA dehydrogenases. A mechanistic overview.
  Eur J Biochem, 271, 494-508.  
12592029 B.D.Silverman (2003).
Hydrophobicity of transmembrane proteins: spatially profiling the distribution.
  Protein Sci, 12, 586-599.  
14660787 B.Schmidt, J.McCracken, and S.Ferguson-Miller (2003).
A discrete water exit pathway in the membrane protein cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 100, 15539-15542.  
12851397 C.Koutsoupakis, T.Soulimane, and C.Varotsis (2003).
Docking site dynamics of ba3-cytochrome c oxidase from Thermus thermophilus.
  J Biol Chem, 278, 36806-36809.  
14517901 E.Arevalo, R.Estephan, J.Madeo, B.Arshava, M.Dumont, J.M.Becker, and F.Naider (2003).
Biosynthesis and biophysical analysis of domains of a yeast G protein-coupled receptor.
  Biopolymers, 71, 516-531.  
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
12655050 E.Kim, M.E.Helton, I.M.Wasser, K.D.Karlin, S.Lu, H.W.Huang, P.Moenne-Loccoz, C.D.Incarvito, A.L.Rheingold, M.Honecker, S.Kaderli, and A.D.Zuberbuhler (2003).
Superoxo, mu-peroxo, and mu-oxo complexes from heme/O2 and heme-Cu/O2 reactivity: copper ligand influences in cytochrome c oxidase models.
  Proc Natl Acad Sci U S A, 100, 3623-3628.  
12637529 E.Pinakoulaki, U.Pfitzner, B.Ludwig, and C.Varotsis (2003).
Direct detection of Fe(IV)[double bond]O intermediates in the cytochrome aa3 oxidase from Paracoccus denitrificans/H2O2 reaction.
  J Biol Chem, 278, 18761-18766.  
12594218 K.Koutsoupakis, S.Stavrakis, T.Soulimane, and C.Varotsis (2003).
Oxygen-linked equilibrium CuB-CO species in cytochrome ba3 oxidase from thermus thermophilus. Implications for an oxygen channel ar the CuB site.
  J Biol Chem, 278, 14893-14896.  
14534303 L.L.Pearce, E.L.Bominaar, B.C.Hill, and J.Peterson (2003).
Reversal of cyanide inhibition of cytochrome c oxidase by the auxiliary substrate nitric oxide: an endogenous antidote to cyanide poisoning?
  J Biol Chem, 278, 52139-52145.  
12829500 M.T.Facciotti, V.S.Cheung, D.Nguyen, S.Rouhani, and R.M.Glaeser (2003).
Crystal structure of the bromide-bound D85S mutant of bacteriorhodopsin: principles of ion pumping.
  Biophys J, 85, 451-458.
PDB code: 1mgy
12937163 O.Maneg, B.Ludwig, and F.Malatesta (2003).
Different interaction modes of two cytochrome-c oxidase soluble CuA fragments with their substrates.
  J Biol Chem, 278, 46734-46740.  
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.
  Free Radic Biol Med, 34, 509-520.  
12851460 R.M.Nyquist, D.Heitbrink, C.Bolwien, R.B.Gennis, and J.Heberle (2003).
Direct observation of protonation reactions during the catalytic cycle of cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 100, 8715-8720.  
12799376 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.
  J Biol Chem, 278, 35861-35868.  
14673090 T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, and S.Yoshikawa (2003).
The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
  Proc Natl Acad Sci U S A, 100, 15304-15309.
PDB codes: 1v54 1v55
11959503 B.Byrne, and S.Iwata (2002).
Membrane protein complexes.
  Curr Opin Struct Biol, 12, 239-243.  
12107185 E.Pinakoulaki, T.Soulimane, and C.Varotsis (2002).
Fourier transform infrared (FTIR) and step-scan time-resolved FTIR spectroscopies reveal a unique active site in cytochrome caa3 oxidase from Thermus thermophilus.
  J Biol Chem, 277, 32867-32874.  
12450405 F.Tomson, J.A.Bailey, R.B.Gennis, C.J.Unkefer, Z.Li, L.A.Silks, R.A.Martinez, R.J.Donohoe, R.B.Dyer, and W.H.Woodruff (2002).
Direct infrared detection of the covalently ring linked His-Tyr structure in the active site of the heme-copper oxidases.
  Biochemistry, 41, 14383-14390.  
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.
  J Biol Chem, 277, 32860-32866.  
11933067 L.Adamian, and J.Liang (2002).
Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers.
  Proteins, 47, 209-218.  
11933230 L.Banci, I.Bertini, S.Ciurli, A.Dikiy, J.Dittmer, A.Rosato, G.Sciara, and A.R.Thompsett (2002).
NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.
  Chembiochem, 3, 299-310.
PDB codes: 1k3g 1k3h
12354114 P.Hellwig, T.Soulimane, and W.Mäntele (2002).
Electrochemical, FT-IR and UV/VIS spectroscopic properties of the caa3 oxidase from T. thermophilus.
  Eur J Biochem, 269, 4830-4838.  
11115638 G.Gilderson, A.Aagaard, C.M.Gomes, P.Adelroth, M.Teixeira, and P.Brzezinski (2001).
Kinetics of electron and proton transfer during O(2) reduction in cytochrome aa(3) from A. ambivalens: an enzyme lacking Glu(I-286).
  Biochim Biophys Acta, 1503, 261-270.  
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.  
11337417 M.G.Palmgren (2001).
PLANT PLASMA MEMBRANE H+-ATPases: Powerhouses for Nutrient Uptake.
  Annu Rev Plant Physiol Plant Mol Biol, 52, 817-845.  
11334784 M.M.Pereira, M.Santana, and M.Teixeira (2001).
A novel scenario for the evolution of haem-copper oxygen reductases.
  Biochim Biophys Acta, 1505, 185-208.  
11828443 S.Lecomte, C.Hilleriteau, J.P.Forgerit, M.Revault, M.H.Baron, P.Hildebrandt, and T.Soulimane (2001).
Structural changes of cytochrome c(552) from Thermus thermophilus adsorbed on anionic and hydrophobic surfaces probed by FTIR and 2D-FTIR spectroscopy.
  Chembiochem, 2, 180-189.  
11327887 Suharti, M.J.Strampraad, I.Schröder, and Vries (2001).
A novel copper A containing menaquinol NO reductase from Bacillus azotoformans.
  Biochemistry, 40, 2632-2639.  
11123910 A.Aagaard, G.Gilderson, D.A.Mills, S.Ferguson-Miller, and P.Brzezinski (2000).
Redesign of the proton-pumping machinery of cytochrome c oxidase: proton pumping does not require Glu(I-286).
  Biochemistry, 39, 15847-15850.  
  11152118 T.Soulimane, M.E.Than, M.Dewor, R.Huber, and G.Buse (2000).
Primary structure of a novel subunit in ba3-cytochrome oxidase from Thermus thermophilus.
  Protein Sci, 9, 2068-2073.  
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