mcrA (MTH_1164) encodes the alpha subunit of methyl-coenzyme M reductase isoenzyme I (MCR I) of the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus. MCR is a cytoplasmic alpha2beta2gamma2 heterohexamer that catalyzes the final, methane-forming step of methanogenesis, the reduction of methyl-coenzyme M with coenzyme B to methane and the CoM-S-S-CoB heterodisulfide (EC 2.8.4.1). Each holoenzyme contains two identical active sites, each holding one non-covalently bound nickel porphinoid coenzyme F430 buried at the interface of the alpha, alpha', beta and gamma subunits; the alpha subunit supplies the axial glutamine ligand to the F430 nickel, most of the coenzyme M and coenzyme B contacts, and a set of conserved post-translationally modified active-site residues (thioglycine, methylated His, Arg, Gln and Cys, and didehydroaspartate). Catalysis requires the Ni(I) state of F430 and proceeds through a methyl radical and Ni(II)-thiolate intermediate. mcrA lies in the mcrBDCGA operon, upstream of the mtr operon; it is transcribed mainly in late growth phase, whereas the paralogous isoenzyme MCR II (mrtBDGA) predominates early in batch culture.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (Cytoplasm, by similarity to the M. marburgensis MCR I alpha subunit P11558). MCR is a soluble, highly abundant cytoplasmic enzyme; reports of membrane proximity exist but no MCR subunit has a membrane anchor. Reason: Cytoplasm is the correct location for this soluble enzyme complex. It is consistent with the ISS row for the same term. Possible peripheral membrane association is unresolved and does not warrant a membrane term. Supporting Evidence: file:METTH/mcrA/mcrA-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P11558}. PMID:30951290 However, none of the genes associated with MCR synthesis |
| GO:0005737 cytoplasm | ISS GO_REF:0000024 | ACCEPT | Summary: Curator-judged sequence-similarity transfer from the M. marburgensis MCR I alpha subunit (P11558), a near-identical ortholog in the same genus. Reason: The ortholog is in the same genus and MCR is a soluble cytoplasmic enzyme. This is the same claim as the IEA row and the two reinforce each other. Supporting Evidence: file:METTH/mcrA/mcrA-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P11558}. |
| GO:0015948 methanogenesis | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the MCR alpha-subunit family signatures. MCR catalyzes the terminal methane-forming step, so the subunit directly participates in methanogenesis. Reason: The claim is correct, and MCR is the catalytic enzyme of the final step. However, M. thermautotrophicus Delta H is an obligate hydrogenotroph that grows only on H2 plus CO2, so the methanogenic route MCR I serves in this organism is CO2 reduction. The more specific is_a child GO:0019386 methanogenesis, from carbon dioxide, is supported. The generic InterPro2GO term is appropriate as a family-wide mapping (MCR serves all methanogenic routes), but at gene level the specific route is known. Proposed replacements: methanogenesis, from carbon dioxide Supporting Evidence: PMID:30951290 an archaeon that grows with H2 and CO2 as sole carbon and energy sources, forming methane. PMID:2269306 Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaebacteria. |
| GO:0050524 coenzyme-B sulfoethylthiotransferase activity | EXP PMID:2269306 Two genetically distinct methyl-coenzyme M reductases in Met... | ACCEPT | Summary: Rospert et al. 1990 purified two genetically distinct MCR isoenzymes (MCR I and MCR II) from strains Marburg and Delta H, and N-terminally sequenced their subunits (UniProt cites this paper for the O27232 N-terminus 2-19, function, catalytic activity and subunit composition). The cached record is abstract-only. Reason: The activity of MCR I is well established and the alpha subunit is the F430-bearing catalytic subunit, so enables is appropriate. The abstract does not report the activity assays, but the UniProt curators (who annotated this paper as evidence for function and catalytic activity) read the full text; per project guidelines this experimental annotation is not overruled. The activity is that of the alpha2beta2gamma2 holoenzyme, captured by the NEW complex annotation. Supporting Evidence: PMID:2269306 Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaebacteria. PMID:2269306 MCR II is similar to MCR I in that it is also composed of three different subunits alpha, beta, and gamma file:METTH/mcrA/mcrA-uniprot.txt Evidence={ECO:0000269|PubMed:2269306, ECO:0000269|PubMed:3122735}; |
| GO:0050524 coenzyme-B sulfoethylthiotransferase activity | EXP PMID:3122735 Evidence that the heterodisulfide of coenzyme M and 7-mercap... | ACCEPT | Summary: Bobik et al. 1987 showed in Delta H cell extracts that coenzyme B (HS-HTP) reduces methyl-coenzyme M to CH4 with stoichiometric formation of the CoM-S-S-CoB heterodisulfide, defining the reaction of EC 2.8.4.1. Reason: This paper established the reaction stoichiometry and the heterodisulfide product that define the GO term. It used cell extracts, which contain both MCR I and MCR II, so it does not attribute the activity specifically to the MCR I alpha subunit. It is still consistent with the purified-enzyme data and the structure, and the claim is correct for this gene product. It is the same claim as the other GO:0050524 rows. Supporting Evidence: PMID:3122735 CH4 and CoM-S-S-HTP were produced stoichiometrically in a ratio of 1:1. PMID:3350018 The enzyme was found to catalyze the reduction of methylcoenzyme M (CH3-S-CoM) with N-7-mercaptoheptanoylthreonine phosphate (H-S-HTP = component B) to CH4. |
| GO:0050524 coenzyme-B sulfoethylthiotransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated annotation (ARBA, InterPro, Rhea/EC) for the MCR alpha subunit activity. Reason: The MCR alpha-subunit family (IPR016212) is uniformly the catalytic subunit of methyl-coenzyme M reductase, and active-site architecture is conserved across MCR types. Consistent with the experimental rows. Supporting Evidence: PMID:9367957 two molecules of the nickel porphinoid coenzyme F430 are embedded between the subunits alpha, alpha', beta, and gamma and alpha', alpha, beta', and gamma', forming two identical active sites. PMID:28559298 virtually identical active site architectures reflecting the chemically challenging mechanism of methane formation |
| GO:0044674 methyl coenzyme M reductase complex | IDA PMID:2269306 Two genetically distinct methyl-coenzyme M reductases in Met... | NEW | Summary: McrA is the alpha subunit of the alpha2beta2gamma2 MCR I holoenzyme. Rospert et al. purified MCR I and MCR II from strain Delta H as three-subunit (alpha, beta, gamma) enzymes; the crystal structure shows the hexameric arrangement with active sites formed between alpha, alpha', beta and gamma. Reason: No complex (cellular component) annotation exists. GO:0044674 (verified in OLS; alpha2beta2gamma2 hexamer, is_a transferase complex) captures that the activity is executed by the holoenzyme, with the alpha subunit contributing the F430 ligand and most of the shared active site. Purification of the subunits as one enzyme from this strain supports membership. Supporting Evidence: PMID:2269306 MCR II is similar to MCR I in that it is also composed of three different subunits alpha, beta, and gamma PMID:9367957 is a 300-kilodalton protein organized as a hexamer in an alpha2beta2gamma2 arrangement. file:METTH/mcrA/mcrA-uniprot.txt SUBUNIT: MCR is a hexamer of two alpha, two beta, and two gamma chains, |
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Download this section (compressed HTML)Q: Do MCR I (mcrBDCGA) and MCR II (mrtBDGA) of M. thermautotrophicus differ in kinetic properties or substrate affinity in a way that explains their growth-phase switching, and is there a physiological role for the isoenzyme-specific post-translational modifications?
Q: Should GO have a coenzyme F430 binding term (a nickel tetrapyrrole cofactor) for MCR alpha subunits, rather than relying on generic nickel cation or metal ion binding mappings?
Experiment: Using the genetic system now available for Methanothermobacter, delete mcrA (or the mrt operon) and compare growth, methane formation and the kinetic properties of the remaining isoenzyme under H2-limited and H2-replete conditions.
Hypothesis: MCR I and MCR II are functionally specialized for H2-limited versus H2-replete growth.
Type: Genetic deletion and enzyme characterization
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