BRENDA - Enzyme Database

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)
EC Number
Crystallization
Organism
1.2.2.4
air-oxidized form
Oligotropha carboxidovorans
1.2.5.3
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
1.2.7.4
vapor diffusion, 800 mM KH2PO4, 800 mM NaH2PO4, 2% 2-methyl-2,4-pentanediol, 100 mM HEPES, pH 7.3
Oligotropha carboxidovorans
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.2.5.3
Fe2+
-
Oligotropha carboxidovorans
1.2.5.3
Molybdenum
in air-oxidized CO dehydrogenase, the oxidation state of Mo is +VI
Oligotropha carboxidovorans
1.2.5.3
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
1.2.5.3
[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
1.2.7.4
Molybdenum
molybdopterin-cytosine dinucleotide cofactor is composed of a molybdenum ion with 2 oxo- and 1 hydroxoligand complexed by the enedithiolene group of molybdopterin
Oligotropha carboxidovorans
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.2.2.4
17800
-
2 * 88700, molybdoprotein L, + 2 * 30200, flacoprotein M, + 2 * 17800 iron-sulfur-protein S, crystallization data
Oligotropha carboxidovorans
1.2.2.4
30200
-
2 * 88700, molybdoprotein L, + 2 * 30200, flacoprotein M, + 2 * 17800 iron-sulfur-protein S, crystallization data
Oligotropha carboxidovorans
1.2.2.4
88700
-
2 * 88700, molybdoprotein L, + 2 * 30200, flacoprotein M, + 2 * 17800 iron-sulfur-protein S, crystallization data
Oligotropha carboxidovorans
1.2.7.4
17800
-
L2,M2,S2, 2 * 17800 + 2 * 30200 + 2 * 88700, dimer of heterotrimers, SDS-PAGE, crystal structure
Oligotropha carboxidovorans
1.2.7.4
30200
-
L2,M2,S2, 2 * 17800 + 2 * 30200 + 2 * 88700, dimer of heterotrimers, SDS-PAGE, crystal structure
Oligotropha carboxidovorans
1.2.7.4
88700
-
L2,M2,S2, 2 * 17800 + 2 * 30200 + 2 * 88700, dimer of heterotrimers, SDS-PAGE, crystal structure
Oligotropha carboxidovorans
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.2.7.4
CO + H2O + electron acceptor
Oligotropha carboxidovorans
a proton gradient across the cytoplasmic membrane is generated by channeling the electrons formed via cytochrome b561 into a CO-insensitive respiratory chain
CO2 + reduced electron acceptor
-
Oligotropha carboxidovorans
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.2.2.4
Oligotropha carboxidovorans
-
-
-
1.2.5.3
Oligotropha carboxidovorans
P19919 and P19920 and P19921
genes coxL, coxM, and coxS
-
1.2.7.4
Oligotropha carboxidovorans
-
-
-
Posttranslational Modification
EC Number
Posttranslational Modification
Commentary
Organism
1.2.2.4
molybdoironflavoprotein
molybdenum with three oxygen ligands, molybdopterin-cytosine dinucleotide and S-selanylcysteine at active site
Oligotropha carboxidovorans
Reaction
EC Number
Reaction
Commentary
Organism
1.2.2.4
CO + H2O + 2 ferricytochrome b-561 = CO2 + 2 H+ + 2 ferrocytochrome b-561
mechanism, necessity of S-selanyl-cysteine for catalysis
Oligotropha carboxidovorans
1.2.5.3
CO + a quinone + H2O = CO2 + a quinol
hypothetical reaction mechanism, overview
Oligotropha carboxidovorans
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.2.5.3
CO + a quinone + H2O
-
390482
Oligotropha carboxidovorans
CO2 + a quinol
-
-
-
?
1.2.7.4
CO + H2O + electron acceptor
a proton gradient across the cytoplasmic membrane is generated by channeling the electrons formed via cytochrome b561 into a CO-insensitive respiratory chain
390482
Oligotropha carboxidovorans
CO2 + reduced electron acceptor
-
390482
Oligotropha carboxidovorans
?
Subunits
EC Number
Subunits
Commentary
Organism
1.2.2.4
heterohexamer
2 * 88700, molybdoprotein L, + 2 * 30200, flacoprotein M, + 2 * 17800 iron-sulfur-protein S, crystallization data
Oligotropha carboxidovorans
1.2.5.3
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
1.2.7.4
hexamer
L2,M2,S2, 2 * 17800 + 2 * 30200 + 2 * 88700, dimer of heterotrimers, SDS-PAGE, crystal structure
Oligotropha carboxidovorans
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.2.5.3
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
1.2.5.3
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
1.2.5.3
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
1.2.7.4
flavin adenine dinucleotide
-
Oligotropha carboxidovorans
1.2.7.4
molybdopterin cytosine dinucleotide
cofactor is buried at the center of the L subunit
Oligotropha carboxidovorans
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.2.5.3
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
1.2.5.3
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
1.2.5.3
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
1.2.7.4
flavin adenine dinucleotide
-
Oligotropha carboxidovorans
1.2.7.4
molybdopterin cytosine dinucleotide
cofactor is buried at the center of the L subunit
Oligotropha carboxidovorans
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.2.2.4
air-oxidized form
Oligotropha carboxidovorans
1.2.5.3
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
1.2.7.4
vapor diffusion, 800 mM KH2PO4, 800 mM NaH2PO4, 2% 2-methyl-2,4-pentanediol, 100 mM HEPES, pH 7.3
Oligotropha carboxidovorans
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.2.5.3
Fe2+
-
Oligotropha carboxidovorans
1.2.5.3
Molybdenum
in air-oxidized CO dehydrogenase, the oxidation state of Mo is +VI
Oligotropha carboxidovorans
1.2.5.3
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
1.2.5.3
[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
1.2.7.4
Molybdenum
molybdopterin-cytosine dinucleotide cofactor is composed of a molybdenum ion with 2 oxo- and 1 hydroxoligand complexed by the enedithiolene group of molybdopterin
Oligotropha carboxidovorans
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.2.2.4
17800
-
2 * 88700, molybdoprotein L, + 2 * 30200, flacoprotein M, + 2 * 17800 iron-sulfur-protein S, crystallization data
Oligotropha carboxidovorans
1.2.2.4
30200
-
2 * 88700, molybdoprotein L, + 2 * 30200, flacoprotein M, + 2 * 17800 iron-sulfur-protein S, crystallization data
Oligotropha carboxidovorans
1.2.2.4
88700
-
2 * 88700, molybdoprotein L, + 2 * 30200, flacoprotein M, + 2 * 17800 iron-sulfur-protein S, crystallization data
Oligotropha carboxidovorans
1.2.7.4
17800
-
L2,M2,S2, 2 * 17800 + 2 * 30200 + 2 * 88700, dimer of heterotrimers, SDS-PAGE, crystal structure
Oligotropha carboxidovorans
1.2.7.4
30200
-
L2,M2,S2, 2 * 17800 + 2 * 30200 + 2 * 88700, dimer of heterotrimers, SDS-PAGE, crystal structure
Oligotropha carboxidovorans
1.2.7.4
88700
-
L2,M2,S2, 2 * 17800 + 2 * 30200 + 2 * 88700, dimer of heterotrimers, SDS-PAGE, crystal structure
Oligotropha carboxidovorans
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.2.7.4
CO + H2O + electron acceptor
Oligotropha carboxidovorans
a proton gradient across the cytoplasmic membrane is generated by channeling the electrons formed via cytochrome b561 into a CO-insensitive respiratory chain
CO2 + reduced electron acceptor
-
Oligotropha carboxidovorans
?
Posttranslational Modification (protein specific)
EC Number
Posttranslational Modification
Commentary
Organism
1.2.2.4
molybdoironflavoprotein
molybdenum with three oxygen ligands, molybdopterin-cytosine dinucleotide and S-selanylcysteine at active site
Oligotropha carboxidovorans
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.2.5.3
CO + a quinone + H2O
-
390482
Oligotropha carboxidovorans
CO2 + a quinol
-
-
-
?
1.2.7.4
CO + H2O + electron acceptor
a proton gradient across the cytoplasmic membrane is generated by channeling the electrons formed via cytochrome b561 into a CO-insensitive respiratory chain
390482
Oligotropha carboxidovorans
CO2 + reduced electron acceptor
-
390482
Oligotropha carboxidovorans
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.2.2.4
heterohexamer
2 * 88700, molybdoprotein L, + 2 * 30200, flacoprotein M, + 2 * 17800 iron-sulfur-protein S, crystallization data
Oligotropha carboxidovorans
1.2.5.3
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
1.2.7.4
hexamer
L2,M2,S2, 2 * 17800 + 2 * 30200 + 2 * 88700, dimer of heterotrimers, SDS-PAGE, crystal structure
Oligotropha carboxidovorans
General Information
EC Number
General Information
Commentary
Organism
1.2.5.3
evolution
CO dehydrogenase is a member of the xanthine oxidase family
Oligotropha carboxidovorans
General Information (protein specific)
EC Number
General Information
Commentary
Organism
1.2.5.3
evolution
CO dehydrogenase is a member of the xanthine oxidase family
Oligotropha carboxidovorans