| Topic | Finding (with quantitative values where available) | Evidence source (first author year journal) | URL/DOI | Pub date |
|---|---|---|---|---|
| Target identity | UniProt D9J262 corresponds to **amoA / Nmar_1500**, annotated as ammonia monooxygenase subunit A in *Nitrosopumilus maritimus*; part of the archaeal **amoA-amoC-amoB** gene set encoding the AMO complex. Archaeal AmoA is divergent from bacterial amoA/pmoA homologs but remains within the CuMMO superfamily. (pqac-00000000) | Walker 2010 PNAS | https://doi.org/10.1073/pnas.0913533107 | Apr 2010 |
| Reaction / primary role | AmoA is the A-subunit of **ammonia monooxygenase (AMO)**, the copper-dependent membrane enzyme that catalyzes the **first, rate-limiting step of nitrification**. Canonical reaction assigned to AMO: **NH3 + O2 + 2e− + 2H+ -> NH2OH + H2O**; for AOA, downstream oxidation chemistry differs from bacteria because *N. maritimus* lacks bacterial HAO/cytochrome c machinery. (pqac-00000001, pqac-00000007, pqac-00000000) | Wright 2023 ISME J; Laughlin 2025; Walker 2010 PNAS | https://doi.org/10.1038/s41396-023-01467-0; https://doi.org/10.1073/pnas.0913533107 | Jul 2023; Apr 2010 |
| Substrate specificity notes | Current consensus is that **NH3 rather than NH4+** is the direct AMO substrate; AMO also uses **O2** as cosubstrate. Inference comes from CuMMO biology, whole-cell kinetics, and the observation that AMO substrates/inhibitors are largely **non-polar**, implying a hydrophobic active site. The exact archaeal substrate scope remains incompletely resolved. (pqac-00000001, pqac-00000004, pqac-00000003) | Wright 2023 ISME J; Horak 2013 ISME J | https://doi.org/10.1038/s41396-023-01467-0; https://doi.org/10.1038/ismej.2013.75 | Jul 2023; May 2013 |
| AMO complex composition | Archaeal AMO contains conserved **AmoA, AmoB, AmoC** and likely archaeal-specific partners **AmoX, AmoY, AmoZ**. Proteomics/cross-linking support a more complex archaeal AMO than the bacterial 3-subunit complex, with AmoX/Y/Z conserved and genetically linked/co-regulated with core amo genes in AOA. (pqac-00000005, pqac-00000001, pqac-00000002) | Hodgskiss 2023 ISME J; Wright 2023 ISME J | https://doi.org/10.1038/s41396-023-01367-3; https://doi.org/10.1038/s41396-023-01467-0 | Apr 2023; Jul 2023 |
| Localization / topology | AMO is an **integral membrane** CuMMO complex. Structural inference for archaeal AMO supports an **outward-facing / extracellular active-site orientation** and extracellular domains distinct from bacterial homologs. AmoA contributes to the membrane-embedded trimeric assembly. (pqac-00000001, pqac-00000004, pqac-00000005) | Wright 2023 ISME J; Hodgskiss 2023 ISME J | https://doi.org/10.1038/s41396-023-01467-0; https://doi.org/10.1038/s41396-023-01367-3 | Jul 2023; Apr 2023 |
| Pathway context | *N. maritimus* encodes amoABC but lacks bacterial **hydroxylamine oxidoreductase (HAO)** and cytochrome c proteins, implying a distinct archaeal ammonia-oxidation pathway that likely relies on **multicopper oxidases / blue copper proteins** for electron transfer. (pqac-00000000, pqac-00000001) | Walker 2010 PNAS; Wright 2023 ISME J | https://doi.org/10.1073/pnas.0913533107; https://doi.org/10.1038/s41396-023-01467-0 | Apr 2010; Jul 2023 |
| Key kinetics: apparent Km | Whole-cell ammonia oxidation kinetics for *N. maritimus* SCM1 are exceptionally high-affinity: reported **Km(app) ~0.132-0.134 uM total ammonium (133 nM)**, equivalent to about **~3 nM NH3** under assay conditions; oxygen uptake showed a similar **Km ~0.133 uM**. (pqac-00000008, pqac-00000010, pqac-00000011, pqac-00000012) | Martens-Habbena 2009 Nature; Martens-Habbena 2011 Methods Enzymol | https://doi.org/10.1038/nature08465; https://doi.org/10.1016/b978-0-12-386489-5.00019-1 | Oct 2009; 2011 |
| Key kinetics: specific affinity / threshold / comparison | Specific affinity for reduced nitrogen was reported as **68,700 L g cells−1 h−1**, **>200-fold** above measured AOB values in the comparison set; growth threshold was estimated at **~10-20 nM** ammonium, with substrate depletion below the **10 nM** analytical detection limit. This explains strong adaptation to oligotrophic marine conditions. (pqac-00000012, pqac-00000014, pqac-00000009) | Martens-Habbena 2009 Nature; Martens-Habbena 2011 Methods Enzymol | https://doi.org/10.1038/nature08465; https://doi.org/10.1016/b978-0-12-386489-5.00019-1 | Oct 2009; 2011 |
| Key kinetics: Vmax / growth / stoichiometry | Reported maximum activity values include **Vmax ~0.857 uM N h−1** (annotated in figure) and protein-normalized rates around **29.82 umol N mg protein−1 h−1**; maximum growth rate **0.027 h−1** (doubling time ~**26 h**). Ammonium and oxygen were consumed at **1:1.52** stoichiometry. (pqac-00000008, pqac-00000010, pqac-00000012) | Martens-Habbena 2009 Nature; Martens-Habbena 2011 Methods Enzymol | https://doi.org/10.1038/nature08465; https://doi.org/10.1016/b978-0-12-386489-5.00019-1 | Oct 2009; 2011 |
| Expression under low ammonia | amoA is among the highest per-cell transcripts in *N. maritimus* before transfer to low-ammonia conditions. Under dialysis-bag nanomolar-ammonia growth, amoA transcript abundance decreased only to about **~21%** of pre-transfer levels, indicating continued investment in ammonia oxidation even at environmentally relevant low substrate levels. (pqac-00000018, pqac-00000017) | Nakagawa 2013 Appl Environ Microbiol | https://doi.org/10.1128/AEM.02028-13 | Nov 2013 |
| Transcript copies per cell across conditions | Reported amoA transcript abundances per cell: **batch culture ~1.4-2.6 copies/cell** during early-mid growth, then falling to **0.0473 -> 0.0090 copies/cell** late; **dialysis-bag** cultures from **~2.50 -> ~0.54 copies/cell**; **ammonia starvation** from **~2.50 -> ~0.71 -> ~0.027-0.010 copies/cell**. These data show strong decline under prolonged starvation but persistence under low-ammonia growth. (pqac-00000016) | Nakagawa 2013 Appl Environ Microbiol | https://doi.org/10.1128/AEM.02028-13 | Nov 2013 |
| Proteomic response to Fe limitation | Under Fe limitation, combined AMO subunit signal increased from **1.75% to 2.37% of total proteome LFQ intensity**; **AmoA (Nmar_1500)** increased significantly, **AmoB** ranked among the most intense proteins, while **AmoC** showed no significant change. Study-wide significance threshold: **FDR-adjusted p < 0.05**. (pqac-00000021, pqac-00000022) | Shafiee 2022 Environmental Microbiology | https://doi.org/10.1111/1462-2920.15491 | May 2022 |


*Table: This table summarizes key functional-annotation facts for *Nitrosopumilus maritimus* AmoA (UniProt D9J262/Nmar_1500), including biochemical role, pathway context, localization, kinetics, and expression responses. It is designed as a compact evidence-backed reference for gene-function annotation.*