BRENDA - Enzyme Database
show all sequences of 1.2.5.3

Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S-selanylcysteine

Dobbek, H.; Gremer, L.; Meyer, O.; Huber, R.; Proc. Natl. Acad. Sci. USA 96, 8884-8889 (1999)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
vapor diffusion method using 0.8 M KH2PO4, 0.8 M NaH2PO4, 2% MPD, and 100 mM HEPES, pH 7.3, crystals containing cyanide are cocrystallized in the presence of 4 mM potassium cyanide, X-ray diffraction structure determination and analysis at 2.36-2.5 A resolution
Oligotropha carboxidovorans
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
-
Oligotropha carboxidovorans
Molybdenum
in air-oxidized CO dehydrogenase, the oxidation state of Mo is +VI
Oligotropha carboxidovorans
selenium
necessity of S-selanylcysteine for the catalyzed reaction, the selenium atom of S-selanylcysteine at the active site is located in a distance of 3.7 A from the Mo ion. It is near the equatorial oxo and hydroxo group of the Mo ion
Oligotropha carboxidovorans
[2Fe-2S] cluster
two types of [2Fe-2S] clusters, [2Fe-2S] clusters of type I and type II, the two [2Fe-2S] clusters are located in the S subunit. These prosthetic groups form a pathway for the electrons to the FAD. The C-terminal domain (residues 77-161) carries the proximal [2Fe-2S] cluster. The cluster is buried in CO dehydrogenase about 11 A below the protein surface at the interface between the S and the L subunit and is adjacent to the MCD-molybdenum cofactor. The [2Fe-2S] cluster is located at the N terminus of two alpha-helices that participate in a four-helix bundle of twofold symmetry
Oligotropha carboxidovorans
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Oligotropha carboxidovorans
P19919 and P19920 and P19921
genes coxL, coxM, and coxS
-
Reaction
Reaction
Commentary
Organism
CO + a quinone + H2O = CO2 + a quinol
hypothetical reaction mechanism, overview
Oligotropha carboxidovorans
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
CO + a quinone + H2O
-
390482
Oligotropha carboxidovorans
CO2 + a quinol
-
-
-
?
Subunits
Subunits
Commentary
Organism
heterohexamer
CO dehydrogenase is composed of an 88.7-kDa molybdoprotein (subunit L), a 30.2-kDa flavoprotein (subunit M), and a 17.8-kDa iron-sulfur protein (subunit S). It is organized as a dimer of LMS heterotrimers
Oligotropha carboxidovorans
Cofactor
Cofactor
Commentary
Organism
Structure
FAD
one noncovalently bound FAD molecule per monomer, FAD-binding occurs on the M subunit and requires conformational changes of subunit M introduced through the binding of subunt M to subunits LS. In air-oxidized CO dehydrogenase, the flavin is fully oxidized
Oligotropha carboxidovorans
molybdopterin cofactor
the L subunit carries the molybdenum cofactor, which is a mononuclear complex of Mo and molybdopterin-cytosine dinucleotide (MCD). The latter occurs in a redox state that is reduced by two electrons compared with the fully oxidized state, a tricyclic tetrahydropterin-pyran system. The MCD-molybdenum cofactor is buried at the center of the L subunit and is ligated through a dense network of hydrogen bonds originating from both domains of subunit L. The geometry of the first coordination sphere around the Mo ion is a distorted square pyramid
Oligotropha carboxidovorans
additional information
the enzyme is a molybdo iron-sulfur flavoprotein containing S-selanylcysteine. The redox components of one LMS-structured monomer are the MCD-molybdenum cofactor, composed of a molybdenum ion with two oxo- and one hydroxoligand, complexed by the enedithiolene group of MCD, [2Fe-2S] clusters of type I and type II, and a noncovalently bound FAD molecule
Oligotropha carboxidovorans
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
FAD
one noncovalently bound FAD molecule per monomer, FAD-binding occurs on the M subunit and requires conformational changes of subunit M introduced through the binding of subunt M to subunits LS. In air-oxidized CO dehydrogenase, the flavin is fully oxidized
Oligotropha carboxidovorans
molybdopterin cofactor
the L subunit carries the molybdenum cofactor, which is a mononuclear complex of Mo and molybdopterin-cytosine dinucleotide (MCD). The latter occurs in a redox state that is reduced by two electrons compared with the fully oxidized state, a tricyclic tetrahydropterin-pyran system. The MCD-molybdenum cofactor is buried at the center of the L subunit and is ligated through a dense network of hydrogen bonds originating from both domains of subunit L. The geometry of the first coordination sphere around the Mo ion is a distorted square pyramid
Oligotropha carboxidovorans
additional information
the enzyme is a molybdo iron-sulfur flavoprotein containing S-selanylcysteine. The redox components of one LMS-structured monomer are the MCD-molybdenum cofactor, composed of a molybdenum ion with two oxo- and one hydroxoligand, complexed by the enedithiolene group of MCD, [2Fe-2S] clusters of type I and type II, and a noncovalently bound FAD molecule
Oligotropha carboxidovorans
Crystallization (Commentary) (protein specific)
Crystallization
Organism
vapor diffusion method using 0.8 M KH2PO4, 0.8 M NaH2PO4, 2% MPD, and 100 mM HEPES, pH 7.3, crystals containing cyanide are cocrystallized in the presence of 4 mM potassium cyanide, X-ray diffraction structure determination and analysis at 2.36-2.5 A resolution
Oligotropha carboxidovorans
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
-
Oligotropha carboxidovorans
Molybdenum
in air-oxidized CO dehydrogenase, the oxidation state of Mo is +VI
Oligotropha carboxidovorans
selenium
necessity of S-selanylcysteine for the catalyzed reaction, the selenium atom of S-selanylcysteine at the active site is located in a distance of 3.7 A from the Mo ion. It is near the equatorial oxo and hydroxo group of the Mo ion
Oligotropha carboxidovorans
[2Fe-2S] cluster
two types of [2Fe-2S] clusters, [2Fe-2S] clusters of type I and type II, the two [2Fe-2S] clusters are located in the S subunit. These prosthetic groups form a pathway for the electrons to the FAD. The C-terminal domain (residues 77-161) carries the proximal [2Fe-2S] cluster. The cluster is buried in CO dehydrogenase about 11 A below the protein surface at the interface between the S and the L subunit and is adjacent to the MCD-molybdenum cofactor. The [2Fe-2S] cluster is located at the N terminus of two alpha-helices that participate in a four-helix bundle of twofold symmetry
Oligotropha carboxidovorans
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
CO + a quinone + H2O
-
390482
Oligotropha carboxidovorans
CO2 + a quinol
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
heterohexamer
CO dehydrogenase is composed of an 88.7-kDa molybdoprotein (subunit L), a 30.2-kDa flavoprotein (subunit M), and a 17.8-kDa iron-sulfur protein (subunit S). It is organized as a dimer of LMS heterotrimers
Oligotropha carboxidovorans
General Information
General Information
Commentary
Organism
evolution
CO dehydrogenase is a member of the xanthine oxidase family
Oligotropha carboxidovorans
General Information (protein specific)
General Information
Commentary
Organism
evolution
CO dehydrogenase is a member of the xanthine oxidase family
Oligotropha carboxidovorans
Other publictions for EC 1.2.5.3
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
736514
Hille
The aerobic CO dehydrogenase f ...
Oligotropha carboxidovorans
J. Biol. Inorg. Chem.
20
243-251
2015
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4
4
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735935
Stein
Orbital contributions to CO ox ...
Hydrogenophaga pseudoflava, Oligotropha carboxidovorans
Chem. Commun. (Camb.)
50
1104-1106
2014
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736513
Pelzmann
Insights into the posttranslat ...
Oligotropha carboxidovorans
J. Biol. Inorg. Chem.
19
1399-1414
2014
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736437
Wilcoxen
The hydrogenase activity of th ...
Oligotropha carboxidovorans
J. Biol. Chem.
288
36052-36060
2013
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725197
Wilcoxen
Substitution of silver for cop ...
Oligotropha carboxidovorans
J. Am. Chem. Soc.
133
12934-12936
2011
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735667
Wilcoxen
Reaction of the molybdenum- an ...
, Oligotropha carboxidovorans ATCC 49405
Biochemistry
50
1910-1916
2011
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725052
Nishimura
-
Purification and characterizat ...
Aeropyrum pernix, Aeropyrum pernix TB5
Fish. Sci.
76
999-1006
2010
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725392
Zhang
Kinetic and spectroscopic stud ...
Oligotropha carboxidovorans
J. Biol. Chem.
285
12571-12578
2010
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736301
Gourlay
Paramagnetic active site model ...
Oligotropha carboxidovorans
J. Am. Chem. Soc.
128
2164-2165
2006
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736512
Resch
Structural and functional reco ...
Oligotropha carboxidovorans, Oligotropha carboxidovorans DSM 1227
J. Biol. Inorg. Chem.
10
518-528
2005
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390484
Lorite
Carbon monoxide dehydrogenase ...
Bradyrhizobium japonicum, Bradyrhizobium japonicum 110spc4
Appl. Environ. Microbiol.
66
1871-1876
2000
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656481
Hanzelmann
The effect of intracellular mo ...
Hydrogenophaga pseudoflava, Hydrogenophaga pseudoflava DSM 1084
J. Mol. Biol.
301
1221-1235
2000
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736397
Gremer
Binding of flavin adenine dinu ...
Oligotropha carboxidovorans, Oligotropha carboxidovorans DSM 1227
J. Biol. Chem.
275
1864-1872
2000
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390482
Dobbek
Crystal structure and mechanis ...
Oligotropha carboxidovorans
Proc. Natl. Acad. Sci. USA
96
8884-8889
1999
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390483
Kang
Cloning and molecular characte ...
Hydrogenophaga pseudoflava, Hydrogenophaga pseudoflava DSM 1084
J. Bacteriol.
181
5581-5590
1999
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390479
Schubel
Molecular characterization of ...
Oligotropha carboxidovorans, Oligotropha carboxidovorans OM5
J. Bacteriol.
177
2197-2203
1995
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