AmtB (PP_5233) is a high-affinity ammonium transporter of the Amt/Mep/Rh (ammonia transporter channel) superfamily located in the cytoplasmic (inner) membrane, where it is predicted to form a trimer with each protomer providing an 11-transmembrane-helix channel. It mediates uptake of ammonium across the membrane, scavenging low external ammonium to support nitrogen assimilation under nitrogen-limiting conditions; family members recruit NH4+ at a periplasmic site and conduct it through a hydrophobic pore (with conserved Phe-gate and twin-His motifs), with deprotonation to NH3 and growing evidence for electrogenic transport. In Pseudomonas putida KT2440, amtB is encoded in a glnK-amtB operon together with the PII-family nitrogen signaling protein GlnK; it is strongly induced (tens-of-fold) during nitrogen limitation under control of the NtrC/sigma-54 (RpoN) regulatory system, and, as in other Proteobacteria, AmtB transport activity can be gated post-translationally by GlnK binding to its cytoplasmic face.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: AmtB is a multi-pass cytoplasmic (inner) membrane transporter; plasma membrane localization is correct for this Amt-family protein. Reason: The UniProt record carries eleven RuleBase-predicted transmembrane helices (UniRule RU362002), and the deep research describes AmtB as a cytoplasmic (inner) membrane ammonium transporter of the Amt/Mep/Rh superfamily, whose members are integral inner-membrane trimers. The ARBA component of the UniProt subcellular-location line is not relied on. Supporting Evidence: file:PSEPK/amtB/amtB-deep-research-falcon.md **AmtB** is a cytoplasmic-membrane ammonium transporter of the conserved **Amt/Mep/Rh** superfamily. file:PSEPK/amtB/amtB-uniprot.txt FT TRANSMEM 39..57 |
| GO:0008519 ammonium channel activity | IEA GO_REF:0000120 | ACCEPT | Summary: AmtB is a member of the ammonia transporter channel (TC 1.A.11.2) family; ammonium channel activity is the appropriate molecular function for this protein. Reason: The Amt/Mep/Rh family is the canonical ammonium channel/transporter family, and AmtB carries the IPR001905/IPR018047/IPR024041 (Ammonium_transpt) domains plus the TC 1.A.11.2 family assignment. This is the standard, well-supported molecular function term for AmtB orthologs. Mechanistic debate over passive NH3 conduction versus electrogenic NH4+ transport does not change the family-level MF assignment. Supporting Evidence: file:PSEPK/amtB/amtB-deep-research-falcon.md AmtB is a **cytoplasmic membrane ammonium transporter/channel** of the **Amt/Mep/Rh family**. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: Generic membrane localization; correct but subsumed by the more specific plasma membrane annotation. Reason: GO:0016020 (membrane) is a true but high-level parent of the more informative GO:0005886 (plasma membrane) annotation the gene already carries; per the refinement rule it is replaced by that specific term. Proposed replacements: plasma membrane |
| GO:0072488 ammonium transmembrane transport | IEA GO_REF:0000120 | ACCEPT | Summary: AmtB mediates transport of ammonium across the cytoplasmic membrane; this is the core biological process for the gene. Reason: Consistent with the molecular function (ammonium channel activity) and with KT2440-specific evidence, summarised in the deep research from the Hervas et al. 2008 transcriptome study (PMID:17965157, full text not cached), that amtB is strongly induced under nitrogen limitation in an NtrC-dependent manner to scavenge external ammonium for nitrogen assimilation. Supporting Evidence: file:PSEPK/amtB/amtB-deep-research-falcon.md **Molecular function:** High-affinity ammonium uptake/transport across the cytoplasmic membrane (Amt/Mep/Rh-family transporter). file:PSEPK/amtB/amtB-deep-research-falcon.md **P. putida KT2440 amtB (PP_5233) expression**: ~**62-fold induction** under nitrogen limitation |
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