Subsystem: CO Dehydrogenase

This subsystem's description is:

Distribution, diversity and ecology of
aerobic CO-oxidizing bacteria
Gary M. King and Carolyn F. Weber :
Box 1 | Essence of CO oxidation
Despite its toxicity for multicellular organisms, some bacteria use carbon monoxide (CO) as a carbon and energy source. CO metabolism begins with a reaction that can be considered a thermodynamically favourable disproportionation, resulting in CO
2 and a pair of reducing equivalents (or molecular hydrogen) as products:
CO + H 2O →CO2 + 2H+ + 2e–
There are several fates for the reducing equivalents, depending on the specific CO oxidizer, and these distinguish the main modes of metabolism. In obligate anaerobes, reducing equivalents can be coupled to sulphate reduction to form sulphide (sulphidogenesis), or to CO
2 reduction to form acetate (acetogenesis) or methane (methanogenesis). In addition,
some obligately anaerobic CO oxidizers produce molecular hydrogen as a terminal product.
Aerobic CO oxidizers couple reducing equivalents from CO to oxygen reduction; some can also reduce nitrate to nitrite (dissimilatory nitrate reduction) or nitrate to dinitrogen (denitrification). CO oxidation by these bacteria depends on a molybdenum-containing enzyme, the aerobic CO dehydrogenase (CODH). Three distinct protein subunits (large, medium and small) comprise CODH, which also contains a specific cofactor, molybdenum cytosine dinucleotide (MCD), which orientates a catalytically essential molybdenum atom at the enzyme active site. Two forms
of aerobic CODH have been identified so far. Form I (also called OMP) has been specifically characterized for its ability to oxidize CO. Form II (also called BMS), which is phylogenetically close to, but distinct from, form I, is a putative CODH, the true function of which remains uncertain. In contrast to form II CODH, the active site of form I CODH
contains a unique catalytically essential loop of four amino acids, cysteine, serine, phenylalanine and arginine, and a copper atom linked to the active site cysteine–sulphur and to the molybdenum atom. Reducing equivalents generated by CODH are linked to energy conservation through electron transport proteins (cytochromes), some of which are CO insensitive.
Obligately anaerobic CO oxidizers have a CODH that differs distinctly from the enzyme used by aerobes, in part because it contains nickel instead of molybdenum as a metal cofactor, and because it can be coupled to acetate metabolism58–62.
In some aerobic CO oxidizers, energy conserved from CO metabolism can be used to fix CO
2 for biomass. This process typically involves the Calvin-Benson-Bassham (CBB) cycle, which is based on the enzyme ribulose-1,5- bisphosphate carboxylase/oxygenase. Other aerobic CO oxidizers seem unable to fix CO 2 by the CBB cycle or other mechanisms. In these organisms, CO can provide a supplemental energy source without contributing directly to biomass.

The first cox genes that were sequenced have been referred to
as form I, or OMP (from Oligotropha, Mycobacterium and Pseudomonas) type genes, whereas the latter have been designated form II, or BMS (from Bradyrhizobium, Mesorhizobium and Sinorhizobium), putative cox57. Form II genes encode molybdenum hydroxylases that are phylogenetically closer to form I genes than to other molybdenum hydroxylases57 (FIG. 2). Similar to form I genes, form II coxM (medium subunit) and coxS (small subunit), encode flavoproteins and iron–sulphur pro- teins,respectively. Form II coxL (large subunit) genes are approximately 40–50% similar to form I coxL, and the two forms share several diagnostic amino-acid motifs, including, among others, GGFGXK, QGQHXTX, GSRST and CGTRIN83. However, the active-site con- figurations for form I and form II differ distinctly. An AYXCSFR motif characterizes the form I CODH active site, whereas AYRGAGR characterizes form II (REF. 57). Although the form I active-site configuration seems to be unique to CODH, the form II active site occurs in numerous molybdenum hydroxylases with diverse specificity.

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DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional Notes 

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CD_DCD_FCD_ECODHsCODHm*CODHlCD_GCD_CCD_F?TR?Mob????Hypo
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Distribution, diversity and ecology of
aerobic CO-oxidizing bacteria
Gary M. King and Carolyn F. Weber :
Box 1 | Essence of CO oxidation
Despite its toxicity for multicellular organisms, some bacteria use carbon monoxide (CO) as a carbon and energy source. CO metabolism begins with a reaction that can be considered a thermodynamically favourable disproportionation, resulting in CO
2 and a pair of reducing equivalents (or molecular hydrogen) as products:
CO + H 2O →CO2 + 2H+ + 2e–
There are several fates for the reducing equivalents, depending on the specific CO oxidizer, and these distinguish the main modes of metabolism. In obligate anaerobes, reducing equivalents can be coupled to sulphate reduction to form sulphide (sulphidogenesis), or to CO
2 reduction to form acetate (acetogenesis) or methane (methanogenesis). In addition,
some obligately anaerobic CO oxidizers produce molecular hydrogen as a terminal product.
Aerobic CO oxidizers couple reducing equivalents from CO to oxygen reduction; some can also reduce nitrate to nitrite (dissimilatory nitrate reduction) or nitrate to dinitrogen (denitrification). CO oxidation by these bacteria depends on a molybdenum-containing enzyme, the aerobic CO dehydrogenase (CODH). Three distinct protein subunits (large, medium and small) comprise CODH, which also contains a specific cofactor, molybdenum cytosine dinucleotide (MCD), which orientates a catalytically essential molybdenum atom at the enzyme active site. Two forms
of aerobic CODH have been identified so far. Form I (also called OMP) has been specifically characterized for its ability to oxidize CO. Form II (also called BMS), which is phylogenetically close to, but distinct from, form I, is a putative CODH, the true function of which remains uncertain. In contrast to form II CODH, the active site of form I CODH
contains a unique catalytically essential loop of four amino acids, cysteine, serine, phenylalanine and arginine, and a copper atom linked to the active site cysteine–sulphur and to the molybdenum atom. Reducing equivalents generated by CODH are linked to energy conservation through electron transport proteins (cytochromes), some of which are CO insensitive.
Obligately anaerobic CO oxidizers have a CODH that differs distinctly from the enzyme used by aerobes, in part because it contains nickel instead of molybdenum as a metal cofactor, and because it can be coupled to acetate metabolism58–62.
In some aerobic CO oxidizers, energy conserved from CO metabolism can be used to fix CO
2 for biomass. This process typically involves the Calvin-Benson-Bassham (CBB) cycle, which is based on the enzyme ribulose-1,5- bisphosphate carboxylase/oxygenase. Other aerobic CO oxidizers seem unable to fix CO 2 by the CBB cycle or other mechanisms. In these organisms, CO can provide a supplemental energy source without contributing directly to biomass.

The first cox genes that were sequenced have been referred to
as form I, or OMP (from Oligotropha, Mycobacterium and Pseudomonas) type genes, whereas the latter have been designated form II, or BMS (from Bradyrhizobium, Mesorhizobium and Sinorhizobium), putative cox57. Form II genes encode molybdenum hydroxylases that are phylogenetically closer to form I genes than to other molybdenum hydroxylases57 (FIG. 2). Similar to form I genes, form II coxM (medium subunit) and coxS (small subunit), encode flavoproteins and iron–sulphur pro- teins,respectively. Form II coxL (large subunit) genes are approximately 40–50% similar to form I coxL, and the two forms share several diagnostic amino-acid motifs, including, among others, GGFGXK, QGQHXTX, GSRST and CGTRIN83. However, the active-site con- figurations for form I and form II differ distinctly. An AYXCSFR motif characterizes the form I CODH active site, whereas AYRGAGR characterizes form II (REF. 57). Although the form I active-site configuration seems to be unique to CODH, the form II active site occurs in numerous molybdenum hydroxylases with diverse specificity.
Notes copied from CBSS-314269.3.peg.1840:
In this SS: proteins that have all the motifs were annotated as:
Carbon monoxide dehydrogenase form I, large chain( EC:1.2.99.2 ) (N8)
proteins with at least one first motif and corresponded gene cluster as:Carbon-monoxide dehydrogenase form II, large subunit (EC 1.2.99.2)
Less clear cases with at least one motif (or without motifs-in archaea)left as:Carbon monoxide dehydrogenase large chain (EC 1.2.99.2)