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Information on EC 1.9.3.1 - cytochrome-c oxidase and Organism(s) Paracoccus denitrificans and UniProt Accession P98002

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     1 Oxidoreductases
         1.9 Acting on a heme group of donors
             1.9.3 With oxygen as acceptor
                1.9.3.1 cytochrome-c oxidase
IUBMB Comments
A cytochrome of the a type containing copper. The reduction of O2 to water is accompanied by the extrusion of four protons from the intramitochondrial compartment. Several bacteria appear to contain analogous oxidases.
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This record set is specific for:
Paracoccus denitrificans
UNIPROT: P98002
Word Map
The taxonomic range for the selected organisms is: Paracoccus denitrificans
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
A-protein, Aa3 terminal Oxidase, AED, ba3 cytochrome c oxidase, ba3-type cytochrome c oxidase, caa3 cytochrome c oxidase, caa3-type cytochrome c oxidase, cbb3 cytochrome c oxidase, cbb3-2 oxidase, cbb3-2 terminal oxidase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A-protein
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-
-
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AED
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-
-
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complex IV (mitochondrial electron transport)
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-
-
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COXVIAH
-
-
-
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cytochrome a3
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-
-
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cytochrome aa3
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-
-
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cytochrome c oxidase
Cytochrome caa3
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-
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cytochrome oxidase
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-
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ferrocytochrome c oxidase
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-
-
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Fourth terminal oxidase
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-
-
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IHQ
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-
-
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indophenol oxidase
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-
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indophenolase
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-
-
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NADH cytochrome c oxidase
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-
-
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oxidase, cytochrome
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-
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Polypeptide VIb
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-
-
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SSG
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-
-
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STA
-
-
-
-
VIA*
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-
-
-
VIIaL
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-
-
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VIIIA
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-
-
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VIIIb
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-
-
-
VIIIC
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-
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Warburg's respiratory enzyme
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-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
show the reaction diagram
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
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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redox reaction
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reduction
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SYSTEMATIC NAME
IUBMB Comments
ferrocytochrome-c:oxygen oxidoreductase
A cytochrome of the a type containing copper. The reduction of O2 to water is accompanied by the extrusion of four protons from the intramitochondrial compartment. Several bacteria appear to contain analogous oxidases.
CAS REGISTRY NUMBER
COMMENTARY hide
9001-16-5
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
show the reaction diagram
ferrocytochrome c + O2
ferricytochrome c + H2O
show the reaction diagram
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
show the reaction diagram
oxidized horse heart cytochrome c + H2O
reduced horse heart cytochrome c + O2 + H+
show the reaction diagram
-
-
-
-
?
reduced cytochrome aa3 + O2 + H+
oxidized cytochrome aa3 + H2O
show the reaction diagram
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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
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-
?
reduced cytochrome c + O2 + H+
oxidized cytochrome c + H2O
show the reaction diagram
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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
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-
?
additional information
?
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the enzyme also shows catalase activity
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
show the reaction diagram
ferrocytochrome c + O2 + H+
ferricytochrome c + H2O
show the reaction diagram
additional information
?
-
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the enzyme also shows catalase activity
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Heme a
Heme a3
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
copper
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contains copper
Cu2+
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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+
Iron
-
contains iron
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
CcO immobilized on a metal film
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NO
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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
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0013 - 0.004
cytochrome c
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
20 - 90
cytochrome c
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
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
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 hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
Sequence
COX1B_PARDE
558
12
62439
Swiss-Prot
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23000
-
1 * 45000 + 1 * 28000 + 1 * 23000, SDS-PAGE
28000
45000
86000
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sedimentation analysis
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
trimer
CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D124N
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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
I347Q
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16% activity compared to the wild type enzyme
K354M
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subunit I mutant. Reduction of heme a3 is totally impaired, overall H+ uptake within 10 s is significantly smaller than in the wild-type
R473Q
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16% activity compared to the wild type enzyme
R474Q
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41% activity compared to the wild type enzyme
R54M
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low turnover number, changes in spectral properties of heme a, lowered midpoint redox potential, electron transfer from CuA to heme a is impaired
T50A
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90% activity compared to the wild type enzyme
T50N
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50% activity compared to the wild type enzyme
V279I
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50% activity compared to the wild type enzyme
Y280H
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catalytic site retains its active configuration that allows O2 binding to heme a3
Y339F
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64% activity compared to the wild type enzyme
Y406F
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40% activity compared to the wild type enzyme
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-70°C, 10 mM Tris-HCl buffer, pH 7.3, 0.1% cholate
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PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
literature overview
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native four-subunit CcO aa3
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one-subunit enzyme, fully active
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Strep-Tactin column chromatography
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wild-type and Y280H mutant enzyme
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli DH5alpha cells
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
reconstitution into phospholipid vesicles
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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 sp. PS3, Bacillus subtilis, Paracoccus denitrificans, Rhodobacter sphaeroides, Thermus thermophilus
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Ludwig, B.
Cytochrome c oxidase in prokaryotes
FEMS Microbiol. Rev.
46
41-56
1987
Bacillus sp. PS3, Bacillus subtilis, Bacteria, Nitrobacter winogradskyi, no activity in Escherichia coli, Paracoccus denitrificans, Rhodobacter capsulatus, Rhodobacter sphaeroides, Starkeya novella, Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
Manually annotated by BRENDA team
Ludwig, B.
Heme aa3-type cytochrome c oxidases from bacteria
Biochim. Biophys. Acta
594
177-189
1980
Bacillus sp. PS3, Bacteria, Bos taurus, Nitrobacter winogradskyi, Paracoccus denitrificans, Starkeya novella, Thermus thermophilus
Manually annotated by BRENDA team
Holm, L.; Saraste, M.; Wikström, M.
Structural models of the redox centres in cytochrome oxidase
EMBO J.
6
2819-2823
1987
Paracoccus denitrificans
Manually annotated by BRENDA team
Muller, M.; Schläpfer, 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
Manually annotated by BRENDA team
Haltia, T.; Puustinen, A.; Finel, M.
The Paracoccus denitrificans cytochrome aa3 has a third subunit
Eur. J. Biochem.
172
543-546
1988
Paracoccus denitrificans
Manually annotated by BRENDA team
Ludwig, B.
Cytochrome c oxidase from Paracoccus denitrificans
Methods Enzymol.
126
153-159
1986
Paracoccus denitrificans
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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, Paracoccus denitrificans, Rhodobacter sphaeroides
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
-
Manually annotated by BRENDA team
Soloviov, M.; Meuwly, M.
CO-dynamics in the active site of cytochrome c oxidase
J. Chem. Phys.
140
145101
2014
Paracoccus denitrificans (P98002)
Manually annotated by BRENDA team
Lu, J.; Gunner, M.R.
Characterizing the proton loading site in cytochrome c oxidase
Proc. Natl. Acad. Sci. USA
111
12414-12419
2014
Bos taurus, Bos taurus (P00396), Paracoccus denitrificans (P98002), Paracoccus denitrificans, Rhodobacter sphaeroides (P33517), Rhodobacter sphaeroides
Manually annotated by BRENDA team
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