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Information on EC 7.1.1.9 - cytochrome-c oxidase and Organism(s) Paracoccus denitrificans and UniProt Accession P98002
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7.1.1.9 cytochrome-c oxidaseIUBMB Comments
An oligomeric membrane heme-Cu:O2 reductase-type enzyme that terminates the respiratory chains of aerobic and facultative aerobic organisms. The reduction of O2 to water is accompanied by the extrusion of four protons. The cytochrome-aa3 enzymes of mitochondria and many bacterial species are the most abundant group, but other variations, such as the bacterial cytochrome-cbb3 enzymes, also exist. All of the variants have a conserved catalytic core subunit (subunit I) that contains a low-spin heme (of a- or b-type), a binuclear metal centre composed of a high-spin heme iron (of a-, o-, or b-type heme, referred to as a3, o3 or b3 heme), and a Cu atom (CuB). Besides subunit I, the enzyme usually has at least two other core subunits: subunit II is the primary electron acceptor; subunit III usually does not contain any cofactors, but in the case of cbb3-type enzymes it is a diheme c-type cytochrome. While most bacterial enzymes consist of only 3--4 subunits, the mitochondrial enzyme is much more complex and contains 14 subunits.
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The taxonomic range for the selected organisms is: Paracoccus denitrificans
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
4
+
+
4
=
4
+
2
4
+
+
8
=
4
+
2
+
4
Synonyms
cytochrome c oxidase, cytochrome oxidase, complex iv, cytochrome c oxidase subunit i, cytochrome c oxidase subunit 1, cytochrome aa3, cytochrome-c oxidase, coxii, cytochrome a3, cox ii, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
CCO
complex IV (mitochondrial electron transport)
-
-
-
-
COXVIAH
-
-
-
-
cytochrome a3
-
-
-
-
cytochrome aa3
-
-
-
-
cytochrome ba3
-
-
-
-
cytochrome bb3
-
-
-
-
cytochrome c oxidase
Cytochrome caa3
-
-
-
-
cytochrome cbb3
-
-
-
-
ferrocytochrome c oxidase
-
-
-
-
indophenol oxidase
-
-
-
-
indophenolase
-
-
-
-
oxidase, cytochrome
-
-
-
-
Warburg's respiratory enzyme
-
-
-
-
cytochrome c oxidase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
spectra of the A, PM, F and O itnermediate state of enzyme catalysis by use of a special cuvette to measure optical changes of millisecond freeze-hyperquench powder samples at temperatures below -23°C. Catalytic cycle of cytochrome c oxidase at low temperature is similar to that at room temperature
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
-
oxidation
-
-
-
-
reduction
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -, -, -, -, -, -
SYSTEMATIC NAME
IUBMB Comments
ferrocytochrome-c:oxygen oxidoreductase
An oligomeric membrane heme-Cu:O2 reductase-type enzyme that terminates the respiratory chains of aerobic and facultative aerobic organisms. The reduction of O2 to water is accompanied by the extrusion of four protons. The cytochrome-aa3 enzymes of mitochondria and many bacterial species are the most abundant group, but other variations, such as the bacterial cytochrome-cbb3 enzymes, also exist. All of the variants have a conserved catalytic core subunit (subunit I) that contains a low-spin heme (of a- or b-type), a binuclear metal centre composed of a high-spin heme iron (of a-, o-, or b-type heme, referred to as a3, o3 or b3 heme), and a Cu atom (CuB). Besides subunit I, the enzyme usually has at least two other core subunits: subunit II is the primary electron acceptor; subunit III usually does not contain any cofactors, but in the case of cbb3-type enzymes it is a diheme c-type cytochrome. While most bacterial enzymes consist of only 3--4 subunits, the mitochondrial enzyme is much more complex and contains 14 subunits.
CAS REGISTRY NUMBER
COMMENTARY
9001-16-5
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
oxidized horse heart cytochrome c + H2O
reduced horse heart cytochrome c + O2 + H+
-
-
-
-
?
reduced cytochrome aa3 + O2 + H+
oxidized cytochrome aa3 + H2O
-
formation of a tryptophan-radical intermediate (tryptophan neutral radical of the strictly conserved Trp-272). The formation of the Trp-272 constitutes the major rate-determining step of the catalytic cycle
-
-
?
reduced cytochrome c + O2 + H+
oxidized cytochrome c + H2O
-
electron exchange of cytochrome c with the electrode with CcO (with a his-tag at the C-terminus of subunit I) immobilized in a protein-tethered bilayer lipid membrane is shown to be mediated by the enzyme if oxygen is present in the bulk solution. The increasing current density in the anodic and cathodic direction in the presence of oxygen may be due to intermediate redox states of the CcO. Hopping mechanism of electron transfer through the enzyme between cytochrome c and the electrode
-
-
?
additional information
?
-
-
the enzyme also shows catalase activity
-
-
?
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
-
-
-
?
ferrocytochrome c + O2
ferricytochrome c + H2O
-
horse ferrocytochrome c
-
-
?
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
-
-
-
-
?
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
-
-
-
-
r
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
the enzyme also shows catalase activity
-
-
?
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
-
-
-
?
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
-
-
-
-
?
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
heme a
-
CuA and heme a are in electronic equilibrium acting as a redox pair
Heme a3
-
Trp-272 is the direct reductant either to the heme a3 oxoferryl species or to CuB2+
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Cu2+
Fe3+
Cu
Cu2+
-
CuA and heme a are in electronic equilibrium acting as a redox pair. Trp-272 is the direct reductant either to the heme a3 oxoferryl species or to CuB2+
Cu
-
CuB located in subunit I, electron flow from ferrocytochrome c to binuclear center
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NO
-
is able to bind two NO molecules in its active site. NO is expected to have only a marginal regulatory role at the level of CcO aa
additional information
-
CcO immobilized on a metal film can be activated by cytochrome c oxidation/reduction
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0013
ferrocytochrome c
-
horse heart cytochrome c, chymotrypsin treated enzyme
0.0017
ferrocytochrome c
-
horse heart cytochrome c, in the presence of 0.1% Triton X-100 and 2 mg/ml asolectin, chymotrypsin treated enzyme
0.0021
ferrocytochrome c
-
horse heart cytochrome c, in the presence of 0.1% Triton X-100 and 2 mg/ml asolectin
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
study of reaction kinetics assuming a fast protonic phase with a proton transfer to H291 and a slow process with a proton transfer to OH-group of binuclear catalytic site. Comparison with kinetics of enzyme from Rhodobacter spaeroides and Bos taurus
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
spectra of the A, PM, F and O inermediate state of enzyme catalysis by use of a special cuvette to measure optical changes of millisecond freeze-hyperquench powder samples at temperatures below -23°C.Catalytic cycle of cytochrome c oxidase at low temperature is similar to that at room temperature
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
28000
45000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
trimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D124N
-
subunit I mutant. Reduction of heme a3-CuB is severely impaired, about 0.8 H+ is promptly bound synchronously with the reduction of heme a, followed by a much slower protonation associated with the retarded reduction of the heme a3-CuB site
K354M
-
subunit I mutant. Reduction of heme a3 is totally impaired, overall H+ uptake within 10 s is significantly smaller than in the wild-type
R54M
-
low turnover number, changes in spectral properties of heme a, lowered midpoint redox potential, electron transfer from CuA to heme a is impaired
Y280H
-
catalytic site retains its active configuration that allows O2 binding to heme a3
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Poole, R.K.
Bacterial cytochrome oxidases. A structurally and functionally diverse group of electron-transfer proteins
Biochim. Biophys. Acta
726
205-243
1983
Bacillus cereus, Bacillus subtilis, Thermus thermophilus, Paracoccus denitrificans, Cereibacter sphaeroides, Bacillus sp. PS3
Chan, S.I.; Li, P.M.
Cytochrome c oxidase: understanding natures design of a proton pump
Biochemistry
29
1-12
1990
Bacteria, eukaryota, Mammalia, Paracoccus denitrificans
Brunori, M.; Antonini, G.; Malatesta, F.; Sarti, P.; Wilson, M.T.
Cytochrome-c oxidase. Subunit structure and proton pumping
Eur. J. Biochem.
169
1-8
1987
Bacteria, Bos taurus, Mammalia, Paracoccus denitrificans
Ludwig, B.
Cytochrome c oxidase in prokaryotes
FEMS Microbiol. Rev.
46
41-56
1987
Bacillus subtilis, Bacteria, Thermus thermophilus, Paracoccus denitrificans, Nitrobacter winogradskyi, no activity in Escherichia coli, Rhodobacter capsulatus, Cereibacter sphaeroides, Starkeya novella, Bacillus sp. PS3, Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
Ludwig, B.
Heme aa3-type cytochrome c oxidases from bacteria
Biochim. Biophys. Acta
594
177-189
1980
Bacteria, Bos taurus, Thermus thermophilus, Paracoccus denitrificans, Nitrobacter winogradskyi, Starkeya novella, Bacillus sp. PS3
Holm, L.; Saraste, M.; Wikstrm, M.
Structural models of the redox centres in cytochrome oxidase
EMBO J.
6
2819-2823
1987
Paracoccus denitrificans
Muller, M.; Schlpfer, B.; Azzi, A.
Preparation of a one-subunit cytochrome oxidase from Paracoccus denitrificans: spectral analysis and enzymatic activity
Biochemistry
27
7546-7551
1988
Paracoccus denitrificans
Haltia, T.; Puustinen, A.; Finel, M.
The Paracoccus denitrificans cytochrome aa3 has a third subunit
Eur. J. Biochem.
172
543-546
1988
Paracoccus denitrificans
Ludwig, B.
Cytochrome c oxidase from Paracoccus denitrificans
Methods Enzymol.
126
153-159
1986
Paracoccus denitrificans
Jasaitis, A.; Backgren, C.; Morgan, J.E.; Puustinen, A.; Verkhovsky, M.I.; Wikstroem, M.
Electron and Proton Transfer in the Arginine-54-Methionine Mutant of Cytochrome c Oxidase from Paracoccus denitrificans
Biochemistry
40
5269-5274
2001
Paracoccus denitrificans
Pinakoulaki, E.; Pfitzner, U.; Ludwig, B.; Varotsis, C.
The role of the cross-link His-Tyr in the functional properties of the binuclear center in cytochrome c oxidase
J. Biol. Chem.
277
13563-13568
2002
Paracoccus denitrificans
Forte, E.; Scandurra, F.M.; Richter, O.M.; D'Itri, E.; Sarti, P.; Brunori, M.; Ludwig, B.; Giuffre, A.
Proton uptake upon anaerobic reduction of the Paracoccus denitrificans cytochrome c oxidase: a kinetic investigation of the K354M and D124N mutants
Biochemistry
43
2957-2963
2004
Paracoccus denitrificans
Wiertz, F.G.; de Vries, S.
Low-temperature kinetic measurements of microsecond freeze-hyperquench (MHQ) cytochrome oxidase monitored by UV-visible spectroscopy with a newly designed cuvette
Biochem. Soc. Trans.
34
136-138
2006
Paracoccus denitrificans
Medvedev, D.M.; Medvedev, E.S.; Kotelnikov, A.I.; Stuchebrukhov, A.A.
Analysis of the kinetics of the membrane potential generated by cytochrome c oxidase upon single electron injection
Biochim. Biophys. Acta
1710
47-56
2005
Bos taurus, Cereibacter sphaeroides, Paracoccus denitrificans
Pilet, E.; Nitschke, W.; Liebl, U.; Vos, M.H.
Accommodation of NO in the active site of mammalian and bacterial cytochrome c oxidase aa3
Biochim. Biophys. Acta
1767
387-392
2007
Bos taurus, Paracoccus denitrificans
Friedrich, M.G.; Plum, M.A.; Santonicola, M.G.; Kirste, V.U.; Knoll, W.; Ludwig, B.; Naumann, R.L.
In situ monitoring of the catalytic activity of cytochrome C oxidase in a biomimetic architecture
Biophys. J.
95
1500-1510
2008
Paracoccus denitrificans
Wiertz, F.G.; Richter, O.M.; Ludwig, B.; de Vries, S.
Kinetic resolution of a tryptophan-radical intermediate in the reaction cycle of Paracoccus denitrificans cytochrome c oxidase
J. Biol. Chem.
282
31580-31591
2007
Paracoccus denitrificans
Koepke, J.; Olkhova, E.; Angerer, H.; Mueller, H.; Peng, G.; Michel, H.
High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways
Biochim. Biophys. Acta
1787
635-645
2009
Paracoccus denitrificans (P98002 and P08306), Paracoccus denitrificans, Paracoccus denitrificans AO1 (P98002 and P08306)
Ji, H.; Das, T.K.; Puustinen, A.; Wikstroem, M.; Yeh, S.R.; Rousseau, D.L.
Modulation of the active site conformation by site-directed mutagenesis in cytochrome c oxidase from Paracoccus denitrificans
J. Inorg. Biochem.
104
318-323
2010
Paracoccus denitrificans
Kozuch, J.; von der Hocht, I.; Hilbers, F.; Michel, H.; Weidinger, I.M.
Resonance Raman characterization of the ammonia-generated oxo intermediate of cytochrome c oxidase from Paracoccus denitrificans
Biochemistry
52
6197-6202
2013
Paracoccus denitrificans
Hilbers, F.; Von Der Hocht, I.; Ludwig, B.; Michel, H.
True wild type and recombinant wild type cytochrome c oxidase from Paracoccus denitrificans show a 20-fold difference in their catalase activity
Biochim. Biophys. Acta
1827
319-327
2013
Paracoccus denitrificans
-
Soloviov, M.; Meuwly, M.
CO-dynamics in the active site of cytochrome c oxidase
J. Chem. Phys.
140
145101
2014
Paracoccus denitrificans (P98002)
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