KdpB is the catalytic ATP-binding subunit of the KdpFABC high-affinity potassium uptake system in N. vulgaris Hildenborough (DVU_3338). As a P-type ATPase (EC 7.2.2.6), KdpB hydrolyzes ATP and forms an aspartyl-phosphate intermediate (Asp302) during the E1/E2 catalytic cycle, driving K+ translocation across the inner membrane. The KdpFABC complex is induced under severe K+ limitation and provides high-affinity K+ uptake (apparent Km ~2 uM). KdpB couples ATP hydrolysis to conformational changes that drive K+ transport through a ~40 A tunnel from the KdpA selectivity filter to the cytoplasmic release site in KdpB.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0071805 potassium ion transmembrane transport | IEA GO_REF:0000108 | ACCEPT | Summary: KdpB is the catalytic subunit of the KdpFABC high-affinity K+ pump that drives potassium ion transmembrane transport. This annotation is correctly inferred from the GO:0008556 molecular function annotation via logical inference. Reason: KdpB is definitively involved in potassium ion transmembrane transport as the ATP-hydrolyzing catalytic subunit of KdpFABC. The UniProt function annotation explicitly states this is a high-affinity ATP-driven potassium transport system. This is the primary biological process for this protein. Supporting Evidence: file:DESVH/Q725T7/Q725T7-deep-research-falcon.md KdpB hydrolyzes ATP and cycles through E1/E2 conformations with a catalytic aspartyl phosphate, driving K+ translocation across the inner membrane |
| GO:0000166 nucleotide binding | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: KdpB binds nucleotides (specifically ATP) as part of its P-type ATPase catalytic mechanism. This is correct but overly general - GO:0005524 (ATP binding) is also annotated and is more specific and informative. Reason: While technically correct (KdpB does bind nucleotides), this annotation is redundant with the more specific GO:0005524 (ATP binding) annotation. The protein specifically binds ATP at defined residues. For annotation parsimony, the more specific ATP binding term is preferred. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-Rule:MF_00285} |
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | ACCEPT | Summary: KdpB requires Mg2+ as a cofactor for ATP hydrolysis, as is typical for P-type ATPases. UniProt annotation identifies Mg2+ binding sites at positions 514 and 518. This is a core function required for catalysis. Reason: Magnesium ion binding is essential for P-type ATPase catalytic function. The Mg2+ cofactor is required for ATP hydrolysis. UniProt HAMAP annotation identifies specific Mg2+ binding residues (positions 514 and 518) in KdpB. This represents a genuine molecular function of the protein. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00285} |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: KdpB is the ATP-binding catalytic subunit of KdpFABC. ATP binding is essential for its P-type ATPase function. Multiple ATP binding residues are annotated in UniProt (339, 343, 371-378, 389). This is a core molecular function. Reason: ATP binding is fundamental to KdpB's function as a P-type ATPase. The protein hydrolyzes ATP to drive K+ transport. The catalytic reaction is: ATP + H2O + K+(out) = ADP + phosphate + K+(in) (EC 7.2.2.6). ATP binding is clearly a core molecular function that should be retained. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-Rule:MF_00285} |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: KdpB localizes to the inner membrane (equivalent to plasma membrane in bacteria). UniProt annotation confirms cell inner membrane localization as a multi-pass membrane protein with 7 transmembrane helices. Reason: KdpFABC is an inner membrane complex in bacteria. UniProt explicitly annotates KdpB as localized to the cell inner membrane. The protein has 7 transmembrane helices. For bacteria, plasma membrane and inner membrane are equivalent terms. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Cell inner membrane {ECO:0000256|HAMAP-Rule:MF_00285} |
| GO:0006811 monoatomic ion transport | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: KdpB is involved in monoatomic ion transport (specifically K+). However, this term is overly general when more specific terms (GO:0006813 potassium ion transport, GO:0071805 potassium ion transmembrane transport) are also annotated. Reason: While technically correct, this annotation is redundant with the more specific GO:0006813 (potassium ion transport) and GO:0071805 (potassium ion transmembrane transport) annotations. KdpB specifically transports K+, not generic ions. The more specific BP terms should be preferred for annotation parsimony. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Ion transport {ECO:0000256|ARBA:ARBA00023065, ECO:0000256|HAMAP-Rule:MF_00285} |
| GO:0006813 potassium ion transport | IEA GO_REF:0000120 | ACCEPT | Summary: KdpB is the catalytic subunit of the high-affinity K+ uptake system KdpFABC. Potassium ion transport is the core biological process. GO:0071805 (potassium ion transmembrane transport) is also annotated and is slightly more specific. Reason: Potassium ion transport is definitively the core biological process of KdpB. While GO:0071805 (potassium ion transmembrane transport) is more specific, retaining both annotations is acceptable as GO:0006813 is a broader parent term that captures the general function. The high-affinity Kdp system is expressed under severe K+ limitation to import K+ into the cytoplasm. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm |
| GO:0008556 P-type potassium transmembrane transporter activity | IEA GO_REF:0000120 | ACCEPT | Summary: GO:0008556 is the most specific and appropriate molecular function term for KdpB. It precisely describes the P-type ATPase mechanism that couples ATP hydrolysis to K+ transport via aspartyl-phosphate intermediate formation. This is the core molecular function annotation. Reason: This is the correct and most informative molecular function term for KdpB. The GO definition matches exactly: "Enables the transfer of K+ from one side of a membrane to the other according to the reaction: ATP + H2O + K+(out) = ADP + phosphate + K+(in)." KdpB forms a 4-aspartylphosphate intermediate at Asp302 during the E1/E2 catalytic cycle, characteristic of P-type ATPases. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Reaction=K(+)(out) + ATP + H2O = K(+)(in) + ADP + phosphate + H(+) |
| GO:0016020 membrane | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: KdpB is a membrane protein with 7 transmembrane helices. However, GO:0005886 (plasma membrane) is more specific and is already annotated. Reason: While correct, this term is redundant with the more specific GO:0005886 (plasma membrane) annotation. The protein is specifically localized to the inner/plasma membrane, not just generically associated with membranes. For annotation parsimony, the more specific CC term is preferred. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Membrane {ECO:0000256|ARBA:ARBA00023136, ECO:0000256|HAMAP-Rule:MF_00285} |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: KdpB has hydrolase activity (hydrolyzes ATP). However, this is an overly generic term when GO:0016887 (ATP hydrolysis activity) is also annotated and provides much more specific information. Reason: This annotation is technically correct but uninformative. KdpB specifically hydrolyzes ATP, not generic substrates. GO:0016887 (ATP hydrolysis activity) is already annotated and is far more informative. The generic "hydrolase activity" term should be avoided in favor of more specific enzyme activity terms. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Hydrolase {ECO:0000313|EMBL:AAS97806.1} |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000002 | ACCEPT | Summary: KdpB hydrolyzes ATP to drive K+ transport. This molecular function is core to the protein's role as a P-type ATPase. The annotation is correct and informative. Reason: ATP hydrolysis is the energy-providing reaction that drives K+ transport in KdpFABC. KdpB is the catalytic subunit responsible for this hydrolysis. The reaction (ATP + H2O = ADP + phosphate) is coupled to conformational changes that translocate K+. This is a core molecular function that should be retained alongside GO:0008556. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: KdpB binds metal ions (specifically Mg2+ as a cofactor). However, GO:0000287 (magnesium ion binding) is more specific and is already annotated. Reason: This annotation is redundant with the more specific GO:0000287 (magnesium ion binding) annotation. KdpB specifically binds Mg2+ as a catalytic cofactor, not generic metal ions. The specific term provides more informative annotation. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-Rule:MF_00285} |
| GO:0031004 potassium ion-transporting ATPase complex | ISO PMID:28636601 Crystal structure of the potassium-importing KdpFABC membran... | NEW | Summary: KdpB is the ATPase subunit of the KdpFABC potassium ion-transporting ATPase complex. Reason: Q725T7 is a full-length KdpB family member (NCBIfam TIGR01497, HAMAP MF_00285) and UniProt's HAMAP rule places it in the three-subunit Kdp system. GO:0031004 is defined as the KdpFABC complex, in which the E. coli ortholog P03960 is the structurally resolved ATPase subunit. No complex term is currently in GOA for this protein. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt The system is composed of three essential subunits: KdpA, KdpB PMID:28636601 This membrane complex, called KdpFABC, has one channel-like subunit (KdpA) belonging to the superfamily of potassium transporters and another pump-like subunit (KdpB) belonging to the superfamily of P-type ATPases. |
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