amoA encodes subunit A of ammonia monooxygenase (AMO), the copper-dependent integral membrane enzyme that catalyses the first and rate-limiting step of nitrification, the oxidation of ammonia to hydroxylamine, in ammonia-oxidizing archaea (Nitrososphaerota). This UniProt entry is a 208-residue partial sequence (fragment) amplified from an environmental clone (SF_AOA_C12) recovered from the biofilter of a marine shrimp recirculating aquaculture system and assigned to the species Nitrosopumilus maritimus; it is not the genome-encoded AmoA of the type strain SCM1. The sequence carries the archaeal AmoA domain (Pfam PF12942) and five predicted transmembrane helices. In ammonia-oxidizing archaea, AmoA is one of the abundant subunits of a membrane-embedded AMO complex that also contains AmoB and AmoC and the archaea-specific subunits AmoX, AmoY and AmoZ; the complex sits in the cytoplasmic (cell) membrane with its active site most likely facing the pseudo-periplasmic space beneath the S-layer. The archaeal enzyme is distantly related to bacterial AMO and to particulate methane monooxygenase (pMMO) within the copper membrane monooxygenase superfamily; no structure of any AMO has been determined, and which subunit carries the catalytic copper site is not known. Whole-cell kinetics of N. maritimus show exceptionally high affinity for ammonium, adapting these archaea to oligotrophic marine waters, where amoA is also the standard molecular marker for ammonia-oxidizing archaea.
Definition: A membrane-embedded protein complex that possesses ammonia monooxygenase activity, catalysing the oxidation of ammonia to hydroxylamine. In ammonia-oxidizing bacteria it contains AmoA, AmoB and AmoC; in ammonia-oxidizing archaea it additionally contains AmoX, AmoY and AmoZ.
Justification: GO has GO:0015050 methane monooxygenase complex for the homologous pMMO but no complex term for AMO. Native-gel proteomics and cross-linking of archaeal membrane complexes now define AMO subunit composition, so AmoA and its partners could be annotated to the complex.
Parent term: oxidoreductase complex
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004497 monooxygenase activity | IEA GO_REF:0000043 | MODIFY | Summary: Keyword-mapped monooxygenase activity. True but general; the specific activity is ammonia monooxygenase activity. This row is no longer in GOA (the October 2026 refresh returns no annotations for D9J262), so it is kept as a retired row. Reason: The two earlier reviews disagreed (ACCEPT vs MODIFY). MODIFY is correct under the project rule that a true but general term is refined rather than accepted: the Archaeal_AmoA domain and family placement identify the substrate as ammonia, and GO:0018597 ammonia monooxygenase activity is an is_a descendant of monooxygenase activity. AmoA is annotated with GO:0018597 as a subunit of the AMO complex, following the convention used for the experimentally characterised bacterial AmoA (AMOA_NITEU, Q04507, GO:0018597 by EXP). The activity is a property of the multi-subunit complex, and which subunit holds the catalytic copper site is unresolved; no AMO structure exists. Proposed replacements: ammonia monooxygenase activity Supporting Evidence: PMID:36721060 step of nitrification is the oxidation of ammonia via the integral membrane protein complex ammonia monooxygenase (AMO) file:NITRP/amoA/amoA-uniprot.txt Pfam; PF12942; Archaeal_AmoA; 1. |
| GO:0005886 plasma membrane | ISS PMID:36721060 Unexpected complexity of the ammonia monooxygenase in archae... | NEW | Summary: AmoA is an integral membrane subunit of AMO in the archaeal cell (cytoplasmic) membrane. Reason: Both earlier reviews proposed NEW GO:0016020 membrane. The sequence has five Phobius-predicted transmembrane helices, and in AOA the AMO subunits are among the most abundant proteins of the membrane fraction. AOA have a single cell membrane surrounded by an S-layer rather than an outer membrane, so the membrane can be specified as the plasma membrane; the active site most likely faces the pseudo-periplasm. This matches the plasma membrane annotation (EXP) of the bacterial AmoA Q04507. The membrane-localisation keyword row (UniProtKB-KW, IEA) that once accompanied this entry is no longer in GOA, so this is proposed as NEW. Supporting Evidence: file:NITRP/amoA/amoA-uniprot.txt TRANSMEM 32..54 PMID:36721060 AMO subunits (AmoA, AmoB, and AmoC) were among the most abundant proteins (22% of iBAQ normalized intensity) detected overall in these membrane fractions. PMID:36721060 rely on a proteinaceous S-layer rather than an outer membrane to create a pseudo-periplasmic space PMID:36721060 These cross-links can rather be attributed to the high abundance of those proteins in the cell membrane. |
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Download this section (compressed HTML)Q: Which AMO subunit carries the catalytic copper site in archaeal AMO, and does AmoA itself bind copper?
Suggested experts: Metalloenzyme biochemists, Structural biologists working on copper membrane monooxygenases
Q: Should GO annotate AMO subunits to a process term for ammonia oxidation? GO:0019329 ammonia oxidation and GO:0019409 aerobic respiration, using ammonia as electron donor currently have no annotations in GOA, not even on the experimentally characterised bacterial AmoA, and the GO:0019409 definition (hydrazine as an intermediate) does not describe aerobic nitrification.
Suggested experts: GO editors, Nitrification biochemists
Q: What sequence positions reliably separate archaeal amoA from bacterial amoA and pmoA in environmental surveys?
Suggested experts: Environmental microbiologists, Phylogeneticists
Experiment: Cryo-EM of the native archaeal AMO complex (AmoABCXYZ) solubilised from Nitrosopumilus or Nitrososphaera membranes, to place the copper sites and define the role of AmoA.
Type: Structural determination
Experiment: Activity-preserving purification or reconstitution of archaeal AMO in nanodiscs, with copper titration and substrate and inhibitor profiling.
Type: Biochemical characterization
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