Information on EC 1.2.5.3 - aerobic carbon monoxide dehydrogenase

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The expected taxonomic range for this enzyme is: Archaea, Bacteria

EC NUMBER
COMMENTARY hide
1.2.5.3
-
RECOMMENDED NAME
GeneOntology No.
aerobic carbon monoxide dehydrogenase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
CO + a quinone + H2O = CO2 + a quinol
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
carbon monoxide oxidation to CO2
-
-
SYSTEMATIC NAME
IUBMB Comments
carbon-monoxide:quinone oxidoreductase
This enzyme, found in carboxydotrophic bacteria, catalyses the oxidation of CO to CO2 under aerobic conditions. The enzyme contains a binuclear Mo-Cu cluster in which the copper is ligated to a molybdopterin center via a sulfur bridge. The enzyme also contains two [2Fe-2S] clusters and FAD, and belongs to the xanthine oxidoreductase family. The CO2 that is produced is assimilated by the Calvin-Benson-Basham cycle, while the electrons are transferred to a quinone via the FAD site, and continue through the electron transfer chain to a dioxygen terminal acceptor [5]. cf. EC 1.2.7.4, anaerobic carbon monoxide dehydrogenase.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
small, medium, and large subunit
B8YAC9 and B8YAC8 and B8YAD0
UniProt
Manually annotated by BRENDA team
small, medium, and large subunit
B8YAC9 and B8YAC8 and B8YAD0
UniProt
Manually annotated by BRENDA team
large, medium, and small subunits; large, medium, and small subunits of CODH are encoded by the structural genes coxL, coxM, and coxS, respectively. They reside on the 128-kb megaplasmid pHCG3
P19919 and P19920 and P19921
UniProt
Manually annotated by BRENDA team
Oligotropha carboxydovorans
genes coxL, coxM, and coxS; genes coxS, coxM, and coxL
P19919 and P19920 and P19921
UniProt
Manually annotated by BRENDA team
Oligotropha carboxydovorans ATCC 49405
genes coxL, coxM, and coxS; genes coxS, coxM, and coxL
P19919 and P19920 and P19921
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
CO + 1,2-naphthoquinone-4-sulfonic acid + H2O
CO2 + 1,2-naphthoquinol-4-sulfonic acid
show the reaction diagram
CO + 1,4-naphthoquinone + H2O
CO2 + 1,4-naphthoquinol
show the reaction diagram
CO + 2-(4-indophenyl)-3-(4-nitrophenyl)-2H-tetrazolium chloride + H2O
CO2 + reduced 2-(4-indophenyl)-3-(4-nitrophenyl)-2H-tetrazolium chloride
show the reaction diagram
CO + a quinone + H2O
CO2 + a quinol
show the reaction diagram
CO + benzoquinone + H2O
CO2 + benzoquinol
show the reaction diagram
CO + methyl viologen + H2O
CO2 + reduced methylene blue
show the reaction diagram
CO + methylene blue + H2O
CO2 + NAD+
show the reaction diagram
CO + NADH + H+ + H2O
CO2 + NADP+
show the reaction diagram
CO + NADPH + H+ + H2O
CO2 + reduced methyl viologen
show the reaction diagram
CO + ubiquinone + H2O
CO2 + ubiquinol
show the reaction diagram
CO + ubiquinone-1 + H2O
CO2 + ubiquinol-1
show the reaction diagram
Oligotropha carboxydovorans
P19919 and P19920 and P19921
-
-
-
?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
CO + a quinone + H2O
CO2 + a quinol
show the reaction diagram
CO + ubiquinone + H2O
CO2 + ubiquinol
show the reaction diagram
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,2-naphthoquinone-4-sulfonic acid
Oligotropha carboxydovorans
P19919 and P19920 and P19921
-
1,4-Naphthoquinone
Oligotropha carboxydovorans
P19919 and P19920 and P19921
-
benzoquinone
methyl viologen
B8YAC9 and B8YAC8 and B8YAD0
-
methylene blue
B8YAC9 and B8YAC8 and B8YAD0
-
Mo/Cu cofactor
P19919 and P19920 and P19921
-
-
molybdenum cofactor
molybdenum-containing cofactor
-
the active site molybdenum center located in teh large subunit. The molybdenum becomes reduced in the final step of the reaction
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molybdopterin cofactor
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NAD+
B8YAC9 and B8YAC8 and B8YAD0
-
NADP+
B8YAC9 and B8YAC8 and B8YAD0
-
phenazine methosulfate
-
artificial electron carrier
quinone
seleno-molybdenum-cofactor
analysis of the architecture and arrangements of the molybdopterin-cytosine dinucleotide-type of the molybdenum cofactor. The hydrogen bonding interaction pattern of the molybdenum cofactor involves 27 hydrogen bonds with the surrounding protein. Of these, eight are with the cytosine moiety, eight with the diphosphate, six with the pyranopterin, and five with the ligands of the Mo. A 5'-CDP residue is present in Mominus CODH, whereas the Mo-pyranopterin moiety is absent. Different side-chain conformations of the active site residues S-selanyl-Cys385 and Glu757 in Moplus and Mominus CODH indicate a side-chain flexibility and a function of the Mo ion in the proper orientation of both residues. Function of the Mo ion in the proper orientation of active-site residues S-selanyl-Cys385 and Glu757. Mo is an absolute requirement for the conversion of molybdopterin to MCD, a tricyclic tetra-hydropterin-pyran system reduced by two electrons when compared to the fully oxidized state, as well as for insertion of the Mo cofactor into CODH
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ubiquinone
P19919 and P19920 and P19921
-
ubiquinone-1
[CuSMoO2] cluster
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CO oxidation by CO dehydrogenase proceeds at a unique [Mo+VIO2-S-Cu+I-S-Cys] cluster which matures posttranslationally while integrated into the completely folded apoenzyme. The Mo ion of the cluster is coordinated by the ene-dithiolate of the molybdopterin cytosine dinucleotide cofactor (MCD). The cofactor biosynthesis starts with the MgATP-dependent, reductive sulfuration of [MoVIO3] to [MoVO2SH] which entails the AAA+-ATPase chaperone CoxD. Then MoV is reoxidized and Cu1+-ion is integrated. Copper is supplied by the soluble CoxF protein which forms a complex with the membrane-bound von Willebrand protein CoxE through RGD-integrin interactions and enables the reduction of CoxF-bound Cu2+, employing electrons from respiration. Copper appears as Cu2+-phytate, is mobilized through the phytase activity of CoxF and then transferred to the CoxF putative copperbinding site. The coxG gene does not participate in the maturation of the bimetallic cluster
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[CuSMoO2] cofactor
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-
-
additional information
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
copper
Fe-S cluster
P19919 and P19920 and P19921
proximal Fe-S cluster I and distal Fe-S cluster II
iron-sulfur center
P19913 and P19914 and P19915
two [2Fe-2S] clusters in the small subunit
Mo2+
-
7.6 mol/mol of enzyme
Mo3+
-
essential for enzyme activity, 1.82 Mo per mol of enzyme dimer
Molybdenum
selenium
[2Fe-2S] cluster
[CuSMoO2] cluster
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
diphenyliodonium chloride
Oligotropha carboxydovorans
P19919 and P19920 and P19921
temporarily, the inhibited flavin diphenyliodonium chloride enzyme complex is slowly returned back to functional enzyme
iodoacetamide
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yields di(carboxamidomethyl)molybdopterin cytosine dinucleotide from reaction with the molybdenum cofactor
n-butylisocyanide
n-butylisonitrile
P19919 and P19920 and P19921
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-
additional information
P19919 and P19920 and P19921
thiol inhibition of CO dehydrogenase
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0107
CO
-
pH 7.2, 25C
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
51.1 - 93.3
CO
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.058
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purified enzyme, pH 7.5, 30C
0.96
B8YAC9 and B8YAC8 and B8YAD0
purified native enzyme, pH 8.0, 95C, using 1 mM methyl blue as electron acceptor
2.1
B8YAC9 and B8YAC8 and B8YAD0
purified native enzyme, pH 8.0, 95C, using 1 mM methyl viologen as electron acceptor
2.45
B8YAC9 and B8YAC8 and B8YAD0
purified native enzyme, pH 8.0, 95C, using 1 mM NADP+ as electron acceptor
2.47
B8YAC9 and B8YAC8 and B8YAD0
purified ative enzyme, pH 8.0, 95C, using 1 mM NAD+ as electron acceptor
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
B8YAC9 and B8YAC8 and B8YAD0
assay at
8.2
P19919 and P19920 and P19921
assay at, reconstituted enzyme
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 10
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only modest loss of activity at these extreme pHs indicates that ionization of functional groups in the active site is not as critical to catalysis for CODH
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25 - 30
Oligotropha carboxydovorans
P19919 and P19920 and P19921
assay at
37
P19919 and P19920 and P19921
assay at, reconstituted enzyme
95
B8YAC9 and B8YAC8 and B8YAD0
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.88
P19913 and P19914 and P19915
large subunit, sequence calculation
7.77
P19913 and P19914 and P19915
small subunit, sequence calculation
8.43
P19913 and P19914 and P19915
medium subunit, sequence calculation
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
-
Oligotropha carboxidovorans is aerobe and able to grow with CO as sole source of both carbon and energy
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
12600
B8YAC9 and B8YAC8 and B8YAD0
LM2S structure, 1 x 86700, large subunit L, + 1 * 34500, medium subunit M, + 1 * 12600, small subunit S, SDS-PAGE
17200
-
(alphabetagamma)2, 2 * 75000, large subunit, + 1 * 28400, medium subunit, + 1 * 17200, small subunit, SDS-PAGE
17752
P19913 and P19914 and P19915
x * 87224, large subunit, + x * 30694, medium subunit, + x * 17752, small subunit, sequence calculation
17800
P19919 and P19920 and P19921
(alphabetagamma)2, 2 * 88700, large subunit, + 2 * 30200, medoum subunit, + 2 * 17800, small subunit, SDS-PAGE
28400
-
(alphabetagamma)2, 2 * 75000, large subunit, + 1 * 28400, medium subunit, + 1 * 17200, small subunit, SDS-PAGE
30000
-
(alphabetagamma)2, 2 * 89000, large subunit, + 1 * 30000, medium subunit, + 1 * 1800, small subunit, SDS-PAGE
30200
P19919 and P19920 and P19921
(alphabetagamma)2, 2 * 88700, large subunit, + 2 * 30200, medoum subunit, + 2 * 17800, small subunit, SDS-PAGE
30694
P19913 and P19914 and P19915
x * 87224, large subunit, + x * 30694, medium subunit, + x * 17752, small subunit, sequence calculation
34500
B8YAC9 and B8YAC8 and B8YAD0
LM2S structure, 1 x 86700, large subunit L, + 1 * 34500, medium subunit M, + 1 * 12600, small subunit S, SDS-PAGE
41000
P19919 and P19920 and P19921
recombinant monomeric deflavo medium subunit, gel filtration
75000
-
(alphabetagamma)2, 2 * 75000, large subunit, + 1 * 28400, medium subunit, + 1 * 17200, small subunit, SDS-PAGE
87224
P19913 and P19914 and P19915
x * 87224, large subunit, + x * 30694, medium subunit, + x * 17752, small subunit, sequence calculation
88700
P19919 and P19920 and P19921
(alphabetagamma)2, 2 * 88700, large subunit, + 2 * 30200, medoum subunit, + 2 * 17800, small subunit, SDS-PAGE
89000
-
(alphabetagamma)2, 2 * 89000, large subunit, + 1 * 30000, medium subunit, + 1 * 1800, small subunit, SDS-PAGE
163700
B8YAC9 and B8YAC8 and B8YAD0
gel filtration
168100
B8YAC9 and B8YAC8 and B8YAD0
about, sequence calculation
230000
-
native PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterohexamer
oligomer
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallization at high (Moplus CODH)cand low intracellular molybdenum content (Mominus CODH), hanging drop vapour-diffusion method, Moplus CODH species at 2.5 units/mg obtained by mixing 0.006 ml of protein in 50 mM Hepes/NaOH, pH 7.2, with 0.002 ml of reservoir solution containing 1.1 M NaK-tartrate, 0.3 M (NH4)H2PO4, pH 7.2, 3% w/v methylpentanediol, and 10 mM dithioerythritol, 1-2 weeks, 4C, from the Mominus CODH species (0.02 units/mg) under the same crystallization conditions only strong bunched crystals in a brown precipitate emerge. Crystals suitable for X-ray data collection are prepared by repeated washing of these crystals with crystallizing agent to remove precipitate, redissolving of crystals in 50 mM Hepes/NaOH followed by recrystallization under the above conditions, X-ray diffraction structure determination and analysis at 2.25 A and 2.35 A resolution, respectively
crystal structure analysis
-
enzyme in complex with inhibitor n-butylisonitrile, PDB ID 1N62, structure analysis
P19919 and P19920 and P19921
purified reconstituted enzyme, hangig drop vapour diffusion method, X-ray diffraction structure determination and analysis at 1.7 A resolution
P19919 and P19920 and P19921
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
P19919 and P19920 and P19921
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
75
B8YAC9 and B8YAC8 and B8YAD0
purifed enzyme, pH 8.0, 10 min, 65% of optimal activity remains
100
B8YAC9 and B8YAC8 and B8YAD0
purifed enzyme, pH 8.0, 10 min, 30% of optimal activity remains
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by anion exchange chromatography and gel filtration
Oligotropha carboxydovorans
P19919 and P19920 and P19921
native enzyme 13fold to homogeneity by ultracentrifugation, anion exchange chromatography, ultrafiltration, hydroxyapatite chromatography, again ultrafiltration, and gel filtration
B8YAC9 and B8YAC8 and B8YAD0
native enzyme 21fold from cell-free extract by ultracentrifugation, anion exchange chroomatography, ultrafiltration, hydrophobic interaction chromatography, ultrafiltration, and gel filtration
-
native enzyme by ammonium sulfate fractionation, dialysis, and anion exchange chromatography, followed by ultrafiltration, and gel filtration
P19913 and P19914 and P19915
recombinant recombinant M subunit 8fold by ultracentrifugation, anion exchange chromatography, and gel filtration from Escherichia coli strain BL21(DE3)
P19919 and P19920 and P19921
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
genes coxS, coxM, and coxL, DNA and amino acid sequence determination and analysis, sequence comparisons with Aeropyrum pernix strain K1, phylogenetic analysis
B8YAC9 and B8YAC8 and B8YAD0
genes coxS, coxM, and coxL, recombinant expression of FAD-reconstituted enzyme and of monomeric deflavo medium subunit in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain DH5alpha
P19919 and P19920 and P19921
genes coxS, coxM, and coxL, the enzyme is encoded by the mega plasmid pHCG3 in the CoxMSL cluster
Oligotropha carboxydovorans
P19919 and P19920 and P19921
genes cutM, cutS, and cutL, gene cluster cutMSL, DNA and amino acid sequence determination and anakysis, sequence comparisons, genetic organization
P19913 and P19914 and P19915
large, medium, and small subunits of CODH are encoded by the structural genes coxL, coxM, and coxS, respectively. They reside on a 128-kb megaplasmid pHCG3, DNA and amino acid sequence determination and analysis, and molecular organization of the coxMSL gene cluster, sequence comparisons
P19919 and P19920 and P19921
the enzyme is encoded by the coxMSL structural genes in the megaplasmid-localized coxBCMSLDEFGHIK gene cluster
P19919 and P19920 and P19921
the enzyme is encoded by the megaplasmid-localized coxBCMSLDEFGHIK gene cluster, the cosMSL structural genes encoding the enzyme
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
reconstitution of 50% enzyme activity by in vitro reconstitution of the active site through the supply of sulfide first and subsequently of Cu(I) under reducing conditions. Immature forms of CO dehydrogenase isolated from the bacterium, which are deficient in S and/or Cu at the active site, are similarly activated. The [CuSMoO2] cluster is properly reconstructed
P19919 and P19920 and P19921