Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

Ammonia-oxidizing archaea and nitrite-oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system

Source study of the D9J262 sequence (UniProt RX line). An environmental amoA survey that classified clones as related to Nitrosopumilus maritimus; it contains no functional assay of the protein.

"Analysis of bacterial and archaeal amoA gene sequences revealed that most ammonia oxidizers were related to Nitrosomonas marina and Nitrosopumilus maritimus."

PMID:36721060

Unexpected complexity of the ammonia monooxygenase in archaea.

Archaeal AMO is an integral membrane complex catalysing the first, rate-limiting step of nitrification.

"step of nitrification is the oxidation of ammonia via the integral membrane protein complex ammonia monooxygenase (AMO)"
Native membrane complexes of two AOA contain AmoA, AmoB, AmoC, AmoX and two new AOA-specific subunits, AmoY and AmoZ.

"Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified."
AmoA, AmoB and AmoC are among the most abundant proteins of the AOA membrane fraction.

"AMO subunits (AmoA, AmoB, and AmoC) were among the most abundant proteins (22% of iBAQ normalized intensity) detected overall in these membrane fractions."
AOA have a single cell membrane and an S-layer that creates a pseudo-periplasm, toward which the AMO active site most likely faces.

"However, it is likely that the active site as well as the soluble AmoB and AmoZ domains are situated toward the pseudo-periplasmic space."
No AMO structure (bacterial or archaeal) has been solved.

"no structural studies have been successfully carried out for any AMO complex, bacterial or archaeal"

PMID:20421470

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.

The N. maritimus SCM1 genome encodes copper-dependent ammonia oxidation and electron transport systems that differ from those of ammonia-oxidizing bacteria.

"revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria"

PMID:19794413

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria.

N. maritimus SCM1 oxidises ammonia with very high affinity.

"Its half-saturation constant (K(m) = 133 nM total ammonium) and substrate threshold"

file:NITRP/amoA/amoA-uniprot.txt

UniProt record for D9J262 (D9J262_9ARCH)

D9J262 is an unreviewed fragment named ammonia monooxygenase subunit A.

"SubName: Full=Ammonia monooxygenase subunit A"
The sequence derives from environmental clone SF_AOA_C12.

"STRAIN=SF_AOA_C12"
The sequence carries the archaeal AmoA Pfam domain.

"Pfam; PF12942; Archaeal_AmoA; 1."
Phobius predicts transmembrane helices (five in total, e.g. residues 32-54).

"TRANSMEM 32..54"

file:NITRP/amoA/amoA-deep-research-falcon.md

Falcon deep research for amoA (D9J262)

Literature synthesis on archaeal AMO (complex composition, copper-centred electron transfer, whole-cell kinetics, transcript and proteome levels of amoA in N. maritimus SCM1).