TABLE 1.
Enzyme lineages included in the phylogenetic analysis, their function and cellular localization, and the amino acids that coordinate the Mo/W liganda
| Mo/W-bisPGD catalytic subunit(s) (abbreviation[s]) | MopB family lineage(s) | Substrate(s) | Function(s) | Cellular localization | Mo/W ligand | Reference(s) |
|---|---|---|---|---|---|---|
| Formyl-methanofuran dehydrogenase subunit B (FwdB/FmdB) | FwdB/FmdB and FhcB (?) | CO2 | Reduces CO2 to formate in hydrogenotrophic methanogenesis | Cytoplasm | Sec/Cys | 141, 142 |
| Formyltransferase/hydrolase subunit B (FhcB) | FwdB/FmdB and FhcB (?) | None | FhcB serves as a scaffold for the catalytic subunits FhcA and FhcD; the Fhc complex generates formate from formyl-H4MPT during growth on 1-carbon compounds | Cytoplasm | Lacks Mo/W-bisPGD | 32 |
| Formate dehydrogenase N subunit G (FdhG) | FdhG | HCOO−1 | Oxidizes formate to CO2 as an electron donor in anaerobic respiration | Periplasm | Sec/Cys | 143 – 145 |
| NAD-dependent formate dehydrogenase | Cytoplasmic formate dehydrogenases | CO2 | Reduces CO2 to formate during acetogenesis | Cytoplasm | Sec/Cys | 146, 147 |
| F420-dependent formate dehydrogenase | Cytoplasmic formate dehydrogenases | HCOO−1 | Oxidizes formate to CO2 during hydrogenotrophic methanogenesis | Cytoplasm | Sec/Cys | 148, 149 |
| Formate hydrogen lyase (FdhH) | Cytoplasmic formate dehydrogenases | HCOO−1 | Oxidizes excess formate to carbon dioxide during fermentative growth | Cytoplasm | Sec/Cys | 150 |
| NAD+ reducing formate dehydrogenase subunit A | Cytoplasmic formate dehydrogenases | HCOO−1 | Oxidizes excess formate to CO2 during aerobic growth | Cytoplasm | Cys | 151 |
| NADH-quinone oxidoreductase subunit 3 (Nqo3) | NAD- and F420-dependent Fdhs, FdhH, and FdsA (?) | NADH | Transfers electrons from NADH to the quinone pool during aerobic respiration | Cytoplasm | Lacks Mo/W-bisPGD | 28 |
| Assimilatory nitrate reductase catalytic subunits (NasC, NasA, and NarB) | NasC, NasA, and NarB | NO3− | Reduce nitrate to nitrite for assimilation into macromolecules | Cytoplasm | Cys | 152 – 154 |
| Arsenite oxidase catalytic subunit (AioA) | AioA and IdrA (?) | AsO33− | Oxidizes arsenite to arsenate as an electron donor in aerobic respiration and anoxygenic photosynthesis | Periplasm | No amino acid ligand | 155, 156 |
| Iodate reductase catalytic subunit (IdrA) | AioA and IdrA (?) | IO3− | Reduces iodate to iodide as the terminal electron acceptor in anaerobic respiration | Periplasm | No amino acid ligand | 9 |
| Periplasmic nitrate reductase catalytic subunit (NapA) | NapA | NO3− | Reduces nitrate to nitrite and can fulfill various physiological functions, including respiration, redox homeostasis, and assimilation | Periplasm | Cys | 157 |
| Acetylene hydratase (AH) | AH (?) | C2H2 | Hydrates acetylene to acetaldehyde during fermentative growth on acetylene | Cytoplasm | Cys | 27 |
| Haloarchaeal dimethyl sulfoxide reductase catalytic subunit (DmsA) | ? | (CH3)2SO and (CH3)3NO | Reduces DMSO and TMAO to DMS and TMA, respectively, during anaerobic respiration | Periplasm | Asp | 158 |
| Perchlorate reductase catalytic subunit (PcrA) | ? | ClO4− | Reduces perchlorate to chlorite as a terminal electron acceptor during anaerobic respiration | Periplasm | Asp | 159, 160 |
| Steroid C25 dehydrogenase catalytic subunit (S25dA) | DdhA, SerA, and EbdA | Steroid C25 | Hydroxylates the C25 atom of steroid molecules to yield sterol C25 during the anaerobic degradation of cholesterol | Periplasm | Asp | 161 |
| p-Cymene dehydrogenase catalytic subunit (CmdA) | DdhA, SerA, and EbdA | p-Cymene | Hydroxylates p-cymene to dimethyl(4-isopropylbenzyl) succinate during the anaerobic degradation of this hydrocarbon | Periplasm | Asp | 162 |
| Ethylbenzene dehydrogenase catalytic subunit (EbdA) | DdhA, SerA, and EbdA | Ethylbenzene | Hydroxylates ethylbenzene to (S)-1-phenylethanol during the anaerobic degradation of ethylbenzene | Periplasm | Asp | 163 |
| Respiratory selenate reductase catalytic subunit (SerA) | DdhA, SerA, and EbdA | SeO42− | Reduces selenate to selenite (SeO32−) as a terminal electron acceptor during anaerobic respiration | Periplasm | Asp | 164 |
| Respiratory chlorate reductase catalytic subunit (ClrA) | DdhA, SerA, and EbdA | ClO3− | Reduces chlorate to chlorite as a terminal electron acceptor during anaerobic respiration | Periplasm | Asp | 165 |
| Dimethyl sulfide dehydrogenase catalytic subunit (DdhA) | DdhA, SerA, and EbdA | (CH3)2S | Oxidizes DMS to DMSO as an electron donor in either anaerobic respiration or anoxygenic photosynthesis | Periplasm | Asp | 166 |
| Respiratory nitrate reductase catalytic subunit (NarG) | NarG | NO3− | Reduces nitrate to nitrite as a terminal electron acceptor during anaerobic respiration | Periplasm or cytoplasm | Asp | 167 – 169 |
| Bacterial dimethyl sulfoxide reductase catalytic subunit | DmsA | (CH3)2SO, (CH3)3NO, and other S- and N-oxides | Reduces DMSO and TMAO to DMS and TMA, respectively, during anaerobic respiration | Periplasm | Ser | 24 |
| Resorcinol hydroxylase catalytic subunit (RhL) | ? | Resorcinol | Hydroxylates the phenolic compound resorcinol to hydroxyhydroquinone as an electron donor in anaerobic respiration | Cytoplasm | Ser | 170 |
| Pyrogallol-phloroglucinol transhydroxylase catalytic subunit (PgtL) | ? | Pyrogallol | Hydroxylates the polyphenolic compound pyrogallol to phloroglucinol during fermentative growth on pyrogallol | Cytoplasm | Ser | 171 |
| Biotin sulfoxide reductase | ? | Biotin-d-sulfoxide and methionine-S-sulfoxide | Converts biotin-d-sulfoxide to d-biotin and methionine-S-sulfoxide to S-methionine so that d-biotin and S-methionine can be recycled as carbon and sulfur sources, respectively | Cytoplasm | Ser | 172 |
| Dimethyl sulfoxide reductase catalytic subunit (DorA) and trimethylamine N-oxide reductase catalytic subunit (TorA) | DorA and TorA | Various S- and N-oxides, including (CH3)2SO and (CH3)3NO | Reduce DMSO to DMS and TMAO to TMA as terminal electron acceptors in anaerobic respiration | Periplasm or cytoplasm | Ser | 173 – 176 |
| Polysulfide reductase catalytic subunit (PsrA) | PsrA, PhsA, and SrrA | Sn2− | Reduces polysulfides to Sn−12− and S2− as terminal electron acceptors in anaerobic respiration | Periplasm | Cys | 177, 178 |
| Thiosulfate reductase catalytic subunit (PhsA) | PsrA, PhsA, and SrrA | S2O32− | Reduces thiosulfate to sulfite (SO32−) and sulfide (S2−) as terminal electron acceptors in anaerobic respiration | Periplasm | Cys | 179, 180 |
| Respiratory selenite reductase catalytic subunit (SrrA) | PsrA, PhsA, and SrrA | SeO32− | Reduces selenite to elemental selenium (Se0) as a terminal electron acceptor in anaerobic respiration | Periplasm | Cys | 181 |
| Archaeal sulfur reductase catalytic subunit (aSreA) | ? | S0 | Reduces elemental sulfur to S2− as a terminal electron acceptor for anaerobic respiration in hyperthermophilic archaea | Periplasm | Cys | 182 |
| Bacterial sulfur reductase catalytic subunit (bSreA) | ? | S0 | Reduces elemental sulfur to S2− as a terminal electron acceptor for anaerobic respiration in hyperthermophilic bacteria | Cytoplasm | Cys | 183 |
| Sulfite oxidase catalytic subunit (SoeA) | ? | SO32− | Oxidizes sulfite to sulfate as an electron donor in anoxygenic photosynthesis | Cytoplasm | Cys | 184 |
| Tetrathionate reductase catalytic subunit (TtrA) | TtrA, SrdA, and archaeal arsenate reductase | S4O62− | Reduces tetrathionate to thiosulfate as a terminal electron acceptor in anaerobic respiration | Periplasm | Cys | 185 |
| Respiratory selenate reductase catalytic subunit (SrdA) | TtrA, SrdA, and archaeal arsenate reductase | SeO42− | Reduces selenate to selenite as a terminal electron acceptor during anaerobic respiration | Periplasm | Cys | 186 |
| Archaeal arsenate reductase catalytic subunit | TtrA, SrdA, and archaeal arsenate reductase | AsO43− | Reduces arsenate to arsenite (AsO33−) as a terminal electron acceptor during anaerobic respiration in some archaea | Periplasm | Cys | 187 |
| Arsenite oxidase catalytic subunit (ArxA) | ArxA and ArrA | AsO33− | Oxidizes arsenite to arsenate as an electron donor in anaerobic respiration or anoxygenic photosynthesis | Periplasm | Cys | 188 |
| Respiratory arsenate reductase catalytic subunit (ArrA) | ArxA and ArrA | AsO43− | Reduces arsenate to arsenite as a terminal electron acceptor in anaerobic respiration | Periplasm | Cys | 189, 190 |
| Alternative complex III subunit B (ActB) | PsrA, PhsA, and SrrA (?) | Unknown | ActB possibly functions to transfer electrons from the ActA and ActE subunits to the menaquinol-oxidizing ActC subunit during aerobic respiration | Periplasm | Lacks Mo/W-bisPGD | 31 |
a
Shown are all of the enzyme families and subfamilies utilized in our phylogenetic analyses; their physiological functions, substrates (if known) and cellular localizations; and the amino acid ligands that position the Mo/W-bisPGD cofactor (if present). Boldface type indicates that the family or subfamily has never been subjected to rigorous phylogenetic analysis. Question marks show that the position of the family or subfamily within the superfamily is unknown or hypothetical. TMA is trimethyl amine.