kdpB

UniProt ID: P03960
Organism: Escherichia coli K-12
Review Status: COMPLETE
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Gene Description

KdpB is the catalytic P-type ATPase subunit (type IA, EC 7.2.2.6) of KdpFABC, the high-affinity, ATP-driven potassium uptake system of the E. coli inner membrane that is expressed under K+ limitation under control of the KdpD/KdpE two-component system. KdpB binds Mg-ATP in its cytoplasmic N and P domains and forms a phosphoenzyme on Asp307 of the DKTGT motif, cycling through E1/E2 conformations while KdpA, KdpC and KdpF remain static. ATP hydrolysis by KdpB is coupled to K+ uptake: K+ is selected by the channel-like KdpA subunit, passes through an intramembrane tunnel to binding sites in the KdpB transmembrane domain, and is released by KdpB to the cytoplasm. KdpC acts as a catalytic chaperone at the KdpB nucleotide-binding loop. KdpB activity is inhibited by phosphorylation of Ser162 in the TGES motif of the A domain.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0000166 nucleotide binding
IEA
GO_REF:0000002
MODIFY
Summary: Nucleotide binding (InterPro P-type ATPase N-domain mapping) is true but general; KdpB binds ATP specifically.
Reason: KdpB binds Mg-ATP in its N/P domains. The informative descendant GO:0005524 ATP binding is already annotated and should replace this general term.
Proposed replacements: ATP binding
Supporting Evidence:
PMID:2849541
and Mg2+-ATP (Km = 80 microM)
PMID:21711450
the KdpC subunit was shown to interact with the nucleotide-binding loop of KdpB in an ATP-dependent manner around the ATP-binding pocket
GO:0000287 magnesium ion binding
IEA
GO_REF:0000104
KEEP AS NON CORE
Summary: Mg2+ is the cofactor of the P-type ATPase reaction; the substrate is Mg-ATP and Mg2+ is coordinated in the P domain.
Reason: Magnesium ion binding is expected for all P-type ATPases (Mg2+ coordinated at the phosphorylation site, Mg-ATP as substrate) and is as specific as warranted, but it is a cofactor requirement rather than the defining function of KdpB.
Supporting Evidence:
PMID:2849541
and Mg2+-ATP (Km = 80 microM)
GO:0005515 protein binding
IPI
PMID:21711450
The KdpC subunit of the Escherichia coli K+-transporting Kdp...
REMOVE
Summary: Interaction of KdpB with KdpC (P03961), which acts as a catalytic chaperone at the KdpB nucleotide-binding loop.
Reason: Bare protein binding is uninformative (project protein-binding policy). The interaction is real but is better captured by KdpB membership of GO:0031004 potassium ion-transporting ATPase complex; removal does not dispute the reported interaction.
Supporting Evidence:
PMID:21711450
the KdpC subunit was shown to interact with the nucleotide-binding loop of KdpB in an ATP-dependent manner around the ATP-binding pocket
GO:0005515 protein binding
IPI
PMID:28636601
Crystal structure of the potassium-importing KdpFABC membran...
REMOVE
Summary: Interaction of KdpB with KdpA (P03959) within the KdpFABC crystal structure.
Reason: Bare protein binding is uninformative (project protein-binding policy). The KdpA-KdpB interface is a subunit contact within KdpFABC, already represented by GO:0031004 complex membership; removal does not dispute the interaction.
Supporting Evidence:
PMID:28636601
Here we report the 2.9 Γ… X-ray structure of the complete Escherichia coli KdpFABC complex
GO:0005524 ATP binding
IEA
GO_REF:0000120
ACCEPT
Summary: KdpB binds ATP in its cytoplasmic N/P domains as substrate for the P-type catalytic cycle.
Reason: ATP binding is directly supported by Mg-ATP kinetics of the purified complex, by the KdpC/KdpB/ATP ternary complex at the KdpB nucleotide-binding loop, and by nucleotide-analogue structures; it is an integral part of KdpB's catalytic function.
Supporting Evidence:
PMID:2849541
and Mg2+-ATP (Km = 80 microM)
PMID:21711450
the KdpC subunit was shown to interact with the nucleotide-binding loop of KdpB in an ATP-dependent manner around the ATP-binding pocket
GO:0005886 plasma membrane
EXP
PMID:2849541
The K+-translocating Kdp-ATPase from Escherichia coli. Purif...
ACCEPT
Summary: KdpB is a multi-pass integral protein of the E. coli inner (plasma) membrane, where the KdpFABC complex resides.
Reason: The Kdp-ATPase was purified from everted inner-membrane vesicles, and anti-KdpB serum inhibited the membrane-bound enzyme.
Supporting Evidence:
PMID:2849541
The Kdp-ATPase complex was purified from everted vesicles
PMID:2849541
the anti-KdpABC and anti-KdpB sera impaired ATPase activity in the membrane-bound as well as in the purified state of the enzyme
GO:0005886 plasma membrane
EXP
PMID:30478378
Cryo-EM structures of KdpFABC suggest a K(+) transport mecha...
ACCEPT
Summary: KdpB is a multi-pass integral protein of the E. coli inner (plasma) membrane, where the KdpFABC complex resides.
Reason: KdpFABC used for cryo-EM was isolated by solubilisation of the membrane fraction; KdpB transmembrane helices form one of the two K+ half-channels.
Supporting Evidence:
PMID:30478378
After cell fractionation, membrane solubilization
PMID:30478378
integrating KdpB directly in the transport process
GO:0005886 plasma membrane
IBA
GO_REF:0000033
ACCEPT
Summary: KdpB is a multi-pass integral protein of the E. coli inner (plasma) membrane, where the KdpFABC complex resides.
Reason: The PAINT inference places inner-membrane localisation at the KdpB family node; this is consistent with direct E. coli evidence (KdpB itself is among the descendant evidences, which is expected and not circular).
Supporting Evidence:
PMID:356049
have been identified and found to be located in the inner membrane
file:ECOLI/kdpB/kdpB-uniprot.txt
This subunit is responsible for energy coupling to the transport system and for the release of the potassium ions to the cytoplasm
GO:0005886 plasma membrane
IDA
PMID:15919996
Global topology analysis of the Escherichia coli inner membr...
ACCEPT
Summary: KdpB is a multi-pass integral protein of the E. coli inner (plasma) membrane, where the KdpFABC complex resides.
Reason: KdpB is among the inner membrane proteins whose C-terminal topology was determined in this global study (abstract-only cache; the curated annotation is deferred to). UniProt cites this paper for the inner-membrane location.
Supporting Evidence:
PMID:15919996
we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins
GO:0005886 plasma membrane
IDA
PMID:28636601
Crystal structure of the potassium-importing KdpFABC membran...
ACCEPT
Summary: KdpB is a multi-pass integral protein of the E. coli inner (plasma) membrane, where the KdpFABC complex resides.
Reason: The crystal structure of the complete membrane complex shows the KdpB transmembrane domain embedded in the membrane together with KdpA, KdpC and KdpF.
Supporting Evidence:
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.
PMID:28636601
Here we report the 2.9 Γ… X-ray structure of the complete Escherichia coli KdpFABC complex
GO:0005886 plasma membrane
IDA
PMID:356049
Identification of the structural proteins of an ATP-driven p...
ACCEPT
Summary: KdpB is a multi-pass integral protein of the E. coli inner (plasma) membrane, where the KdpFABC complex resides.
Reason: The three Kdp structural proteins, including the 90 kDa KdpB, were identified and located in the inner membrane.
Supporting Evidence:
PMID:356049
have been identified and found to be located in the inner membrane
GO:0005886 plasma membrane
IEA
GO_REF:0000120
ACCEPT
Summary: KdpB is a multi-pass integral protein of the E. coli inner (plasma) membrane, where the KdpFABC complex resides.
Reason: Electronic mapping from the UniProt subcellular location (cell inner membrane); fully consistent with experimental data.
Supporting Evidence:
PMID:356049
have been identified and found to be located in the inner membrane
GO:0005886 plasma membrane
ISM
PMID:6146979
Sequence homology between two membrane transport ATPases, th...
ACCEPT
Summary: KdpB is a multi-pass integral protein of the E. coli inner (plasma) membrane, where the KdpFABC complex resides.
Reason: Sequence analysis showed KdpB to be homologous to the membrane Ca2+-ATPase of sarcoplasmic reticulum, consistent with an integral membrane P-type ATPase.
Supporting Evidence:
PMID:6146979
Regions of the predicted amino acid sequence of KdpB, the phosphorylated protein of the system, are homologous to regions of the Ca2+-ATPase of rabbit sarcoplasmic reticulum.
GO:0006813 potassium ion transport
IDA
PMID:28636601
Crystal structure of the potassium-importing KdpFABC membran...
MODIFY
Summary: KdpB is required for, and participates in, Kdp-mediated K+ uptake across the inner membrane.
Reason: The structure defines the K+ pathway from the KdpA selectivity filter to KdpB. Potassium ion transport is correct but general; the Kdp process is specifically transmembrane K+ uptake, so the is_a child GO:0071805 potassium ion transmembrane transport (already carried by KdpB) is the appropriate term.
Supporting Evidence:
PMID:28636601
the mechanism by which uphill potassium transport through KdpA is coupled with ATP hydrolysis by KdpB remains poorly understood
GO:0006813 potassium ion transport
IEA
GO_REF:0000120
MODIFY
Summary: KdpB is required for, and participates in, Kdp-mediated K+ uptake across the inner membrane.
Reason: Electronic mapping from InterPro/UniRule KdpB signatures. Potassium ion transport is correct but general; the Kdp process is specifically transmembrane K+ uptake, so the is_a child GO:0071805 potassium ion transmembrane transport (already carried by KdpB) is the appropriate term.
Supporting Evidence:
file:ECOLI/kdpB/kdpB-uniprot.txt
This subunit is responsible for energy coupling to the transport system and for the release of the potassium ions to the cytoplasm
GO:0006813 potassium ion transport
IMP
PMID:17994765
The conserved dipole in transmembrane helix 5 of KdpB in the...
MODIFY
Summary: KdpB is required for, and participates in, Kdp-mediated K+ uptake across the inner membrane.
Reason: Mutations of the TM5 dipole of KdpB slow growth under K+ limitation and uncouple ATP hydrolysis from K+ transport. Potassium ion transport is correct but general; the Kdp process is specifically transmembrane K+ uptake, so the is_a child GO:0071805 potassium ion transmembrane transport (already carried by KdpB) is the appropriate term.
Supporting Evidence:
PMID:17994765
which are located at the center of transmembrane helix 5 (TM 5) of the catalytic KdpB subunit
PMID:17994765
led to an uncoupling of ATP hydrolysis and K+ transport
GO:0008556 P-type potassium transmembrane transporter activity
EXP
PMID:2849541
The K+-translocating Kdp-ATPase from Escherichia coli. Purif...
ACCEPT
Summary: P-type potassium transmembrane transporter activity (ATP + H2O + K+(out) = ADP + phosphate + K+(in)) is the activity of the KdpFABC complex, in which KdpB is the catalytic, phosphorylated energy-coupling subunit.
Reason: The purified KdpABC complex showed K+-dependent, vanadate-sensitive ATPase activity, and anti-KdpB serum inhibited it. KdpB hydrolyses ATP via an aspartyl-phosphate (Asp307) intermediate, and recent structures place the cytoplasmic K+ release site in KdpB, so KdpB does part of the transport work and not only the energisation. The activity is a complex activity (KdpA supplies the selectivity filter), so core_functions records KdpB as enabling ATP hydrolysis and contributing to GO:0008556; the GOA 'enables' row is accepted because the term is the correct functional characterisation of the pump that KdpB catalyses.
Supporting Evidence:
PMID:2849541
The Kdp system from Escherichia coli is a derepressible high-affinity K+-uptake ATPase.
PMID:2849541
the anti-KdpABC and anti-KdpB sera impaired ATPase activity in the membrane-bound as well as in the purified state of the enzyme
GO:0008556 P-type potassium transmembrane transporter activity
EXP
PMID:34272288
Structural basis for potassium transport in prokaryotes by K...
ACCEPT
Summary: P-type potassium transmembrane transporter activity (ATP + H2O + K+(out) = ADP + phosphate + K+(in)) is the activity of the KdpFABC complex, in which KdpB is the catalytic, phosphorylated energy-coupling subunit.
Reason: Cryo-EM of four reaction-cycle intermediates shows ATP hydrolysis by KdpB coupled to K+ transfer through KdpB sites and release to the cytoplasm. KdpB hydrolyses ATP via an aspartyl-phosphate (Asp307) intermediate, and recent structures place the cytoplasmic K+ release site in KdpB, so KdpB does part of the transport work and not only the energisation. The activity is a complex activity (KdpA supplies the selectivity filter), so core_functions records KdpB as enabling ATP hydrolysis and contributing to GO:0008556; the GOA 'enables' row is accepted because the term is the correct functional characterisation of the pump that KdpB catalyses.
Supporting Evidence:
PMID:34272288
KdpB, on the other hand, harnesses the energy of ATP to drive transport of K + against a concentration gradient
PMID:34272288
Our structures suggest a mechanism where ATP hydrolysis is coupled to K+ transfer between alternative sites in KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K+ to the cytoplasm.
GO:0008556 P-type potassium transmembrane transporter activity
IBA
GO_REF:0000033
ACCEPT
Summary: P-type potassium transmembrane transporter activity (ATP + H2O + K+(out) = ADP + phosphate + K+(in)) is the activity of the KdpFABC complex, in which KdpB is the catalytic, phosphorylated energy-coupling subunit.
Reason: The PAINT node for the KdpB family is well placed; KdpB is the defining subunit of the Kdp P-type ATPase lineage and E. coli KdpB's own experimental data are part of the IBD grounding. KdpB hydrolyses ATP via an aspartyl-phosphate (Asp307) intermediate, and recent structures place the cytoplasmic K+ release site in KdpB, so KdpB does part of the transport work and not only the energisation. The activity is a complex activity (KdpA supplies the selectivity filter), so core_functions records KdpB as enabling ATP hydrolysis and contributing to GO:0008556; the GOA 'enables' row is accepted because the term is the correct functional characterisation of the pump that KdpB catalyses.
Supporting Evidence:
file:ECOLI/kdpB/kdpB-uniprot.txt
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IA subfamily.
file:ECOLI/kdpB/kdpB-uniprot.txt
This subunit is responsible for energy coupling to the transport system and for the release of the potassium ions to the cytoplasm
GO:0008556 P-type potassium transmembrane transporter activity
IDA
PMID:8499455
ATP-driven potassium transport in right-side-out membrane ve...
ACCEPT
Summary: P-type potassium transmembrane transporter activity (ATP + H2O + K+(out) = ADP + phosphate + K+(in)) is the activity of the KdpFABC complex, in which KdpB is the catalytic, phosphorylated energy-coupling subunit.
Reason: ATP generated inside right-side-out vesicles drove vanadate-sensitive K+ uptake via the Kdp-ATPase. KdpB hydrolyses ATP via an aspartyl-phosphate (Asp307) intermediate, and recent structures place the cytoplasmic K+ release site in KdpB, so KdpB does part of the transport work and not only the energisation. The activity is a complex activity (KdpA supplies the selectivity filter), so core_functions records KdpB as enabling ATP hydrolysis and contributing to GO:0008556; the GOA 'enables' row is accepted because the term is the correct functional characterisation of the pump that KdpB catalyses.
Supporting Evidence:
PMID:8499455
This ATP level was sufficient to drive uptake of potassium ions via the Kdp-ATPase.
GO:0008556 P-type potassium transmembrane transporter activity
IDA
PMID:9789555
Structure and function of the Kdp-ATPase of Escherichia coli...
ACCEPT
Summary: P-type potassium transmembrane transporter activity (ATP + H2O + K+(out) = ADP + phosphate + K+(in)) is the activity of the KdpFABC complex, in which KdpB is the catalytic, phosphorylated energy-coupling subunit.
Reason: Reconstituted purified Kdp-ATPase translocated K+ electrogenically on ATP addition. KdpB hydrolyses ATP via an aspartyl-phosphate (Asp307) intermediate, and recent structures place the cytoplasmic K+ release site in KdpB, so KdpB does part of the transport work and not only the energisation. The activity is a complex activity (KdpA supplies the selectivity filter), so core_functions records KdpB as enabling ATP hydrolysis and contributing to GO:0008556; the GOA 'enables' row is accepted because the term is the correct functional characterisation of the pump that KdpB catalyses.
Supporting Evidence:
PMID:9789555
These data clearly indicate that the Kdp-ATPase transports K+ in an electrogenic manner.
GO:0008556 P-type potassium transmembrane transporter activity
IEA
GO_REF:0000120
ACCEPT
Summary: P-type potassium transmembrane transporter activity (ATP + H2O + K+(out) = ADP + phosphate + K+(in)) is the activity of the KdpFABC complex, in which KdpB is the catalytic, phosphorylated energy-coupling subunit.
Reason: Electronic mapping from EC 7.2.2.6/RHEA:16777 and KdpB family signatures (TIGR01497, HAMAP MF_00285). KdpB hydrolyses ATP via an aspartyl-phosphate (Asp307) intermediate, and recent structures place the cytoplasmic K+ release site in KdpB, so KdpB does part of the transport work and not only the energisation. The activity is a complex activity (KdpA supplies the selectivity filter), so core_functions records KdpB as enabling ATP hydrolysis and contributing to GO:0008556; the GOA 'enables' row is accepted because the term is the correct functional characterisation of the pump that KdpB catalyses.
Supporting Evidence:
file:ECOLI/kdpB/kdpB-uniprot.txt
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IA subfamily.
GO:0008556 P-type potassium transmembrane transporter activity
IMP
PMID:17994765
The conserved dipole in transmembrane helix 5 of KdpB in the...
ACCEPT
Summary: P-type potassium transmembrane transporter activity (ATP + H2O + K+(out) = ADP + phosphate + K+(in)) is the activity of the KdpFABC complex, in which KdpB is the catalytic, phosphorylated energy-coupling subunit.
Reason: KdpB TM5 dipole mutants uncouple ATP hydrolysis from K+ transport, showing KdpB is needed for coupled transport. KdpB hydrolyses ATP via an aspartyl-phosphate (Asp307) intermediate, and recent structures place the cytoplasmic K+ release site in KdpB, so KdpB does part of the transport work and not only the energisation. The activity is a complex activity (KdpA supplies the selectivity filter), so core_functions records KdpB as enabling ATP hydrolysis and contributing to GO:0008556; the GOA 'enables' row is accepted because the term is the correct functional characterisation of the pump that KdpB catalyses.
Supporting Evidence:
PMID:17994765
led to an uncoupling of ATP hydrolysis and K+ transport
GO:0016020 membrane
IEA
GO_REF:0000002
MODIFY
Summary: KdpB is a membrane protein; correct but general.
Reason: Membrane is correct but uninformative for this protein; KdpB is specifically an inner (plasma) membrane protein, so the descendant GO:0005886 plasma membrane, already annotated with experimental support, should be used.
Proposed replacements: plasma membrane
Supporting Evidence:
PMID:356049
have been identified and found to be located in the inner membrane
GO:0016887 ATP hydrolysis activity
IEA
GO_REF:0000002
ACCEPT
Summary: KdpB is the ATP-hydrolysing subunit of KdpFABC, forming an Asp307 phosphoenzyme in the P-type cycle.
Reason: ATP hydrolysis is the catalytic activity carried out by KdpB itself (KdpA, KdpC and KdpF are not ATPases). Asp307 substitutions abolish phosphoenzyme formation and ATPase activity, and anti-KdpB antibodies inhibit the enzyme. This is KdpB's direct core molecular function; it is not entailed by GO:0008556 in the ontology.
Supporting Evidence:
PMID:30478378
While ATP hydrolysis is accomplished by the P-type ATPase subunit KdpB
PMID:28636601
the energy of ATP is harnessed by KdpB
file:ECOLI/kdpB/kdpB-uniprot.txt
D->E,N,Q: Unable to form a phosphorylated intermediate and lacks ATPase activity.
PMID:2849541
the anti-KdpABC and anti-KdpB sera impaired ATPase activity in the membrane-bound as well as in the purified state of the enzyme
GO:0031004 potassium ion-transporting ATPase complex
IBA
GO_REF:0000033
ACCEPT
Summary: KdpB is the P-type ATPase subunit of the KdpFABC potassium ion-transporting ATPase complex.
Reason: GO:0031004 is defined as the KdpFABC complex and names KdpB as its ATPase. The PAINT node placement is sound for the conserved KdpB lineage.
Supporting Evidence:
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.
GO:0031004 potassium ion-transporting ATPase complex
IDA
PMID:28636601
Crystal structure of the potassium-importing KdpFABC membran...
ACCEPT
Summary: KdpB is the P-type ATPase subunit of the KdpFABC potassium ion-transporting ATPase complex.
Reason: The 2.9 A crystal structure of the complete E. coli KdpFABC complex directly shows KdpB in the complex.
Supporting Evidence:
PMID:28636601
Here we report the 2.9 Γ… X-ray structure of the complete Escherichia coli KdpFABC complex
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.
GO:0071805 potassium ion transmembrane transport
IBA
GO_REF:0000033
ACCEPT
Summary: KdpB energises and participates in ATP-driven K+ transport across the inner membrane.
Reason: Correct process; KdpB energises and conducts the final step of K+ transmembrane uptake. Sound PAINT placement.
Supporting Evidence:
file:ECOLI/kdpB/kdpB-uniprot.txt
This subunit is responsible for energy coupling to the transport system and for the release of the potassium ions to the cytoplasm
PMID:34272288
Our structures suggest a mechanism where ATP hydrolysis is coupled to K+ transfer between alternative sites in KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K+ to the cytoplasm.
GO:0071805 potassium ion transmembrane transport
IDA
PMID:8499455
ATP-driven potassium transport in right-side-out membrane ve...
ACCEPT
Summary: KdpB energises and participates in ATP-driven K+ transport across the inner membrane.
Reason: ATP-driven K+ uptake into vesicles via the Kdp-ATPase.
Supporting Evidence:
PMID:8499455
This ATP level was sufficient to drive uptake of potassium ions via the Kdp-ATPase.
GO:0071805 potassium ion transmembrane transport
IDA
PMID:9789555
Structure and function of the Kdp-ATPase of Escherichia coli...
ACCEPT
Summary: KdpB energises and participates in ATP-driven K+ transport across the inner membrane.
Reason: Electrogenic K+ translocation by reconstituted Kdp-ATPase.
Supporting Evidence:
PMID:9789555
These data clearly indicate that the Kdp-ATPase transports K+ in an electrogenic manner.
GO:0071805 potassium ion transmembrane transport
IMP
PMID:7896809
Genetic evidence for two sequentially occupied K+ binding si...
ACCEPT
Summary: KdpB energises and participates in ATP-driven K+ transport across the inner membrane.
Reason: Genetic analysis of Kdp K+-affinity mutants (mainly in KdpA) defined the transport pathway and showed that KdpB mediates energy coupling to transport; the acts_upstream_of_or_within qualifier is appropriate (abstract-only cache, curator deferred to).
Supporting Evidence:
PMID:7896809
Energy coupling in Kdp, mediated by the KdpB subunit, is performed by a different subunit from the one that mediates transport.
GO:0098655 monoatomic cation transmembrane transport
IDA
PMID:8499455
ATP-driven potassium transport in right-side-out membrane ve...
MODIFY
Summary: Kdp-ATPase-driven cation uptake in vesicles; the transported cation is K+.
Reason: Monoatomic cation transmembrane transport is correct but general; the transported cation is K+, so the is_a child GO:0071805 potassium ion transmembrane transport (already annotated from the same paper) should be used.
Supporting Evidence:
PMID:8499455
This ATP level was sufficient to drive uptake of potassium ions via the Kdp-ATPase.
GO:1903103 potassium:proton antiporter complex
IBA
GO_REF:0000033
MODIFY
Summary: Complex-membership claim mapped to the wrong complex term: GO:1903103 is a potassium:proton antiporter complex, whereas KdpFABC is a P-type K+-transporting ATPase.
Reason: This IBA propagates the same complex mis-mapping from the experimental KdpB row to the KdpB family node. The complex membership itself is correct; GO:0031004 potassium ion-transporting ATPase complex, whose definition names the E. coli KdpFABC complex, is the right term (already annotated to KdpB by IDA and IBA).
Propagation Review
Root cause: TERM SCOPING PROBLEM
Failure modes: COMPARTMENT OR COMPLEX MISMATCH
Sources checked:
PANTHER:PTN001184736 Β· PTN001184736 SOURCE BAD
The node correctly asserts KdpFABC complex membership, but with the antiporter complex term GO:1903103 rather than GO:0031004; the descendant experimental source is the IPI row from PMID:28636601 carrying the same term mis-mapping.
Supporting Evidence:
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.
PMID:28636601
the energy of ATP is harnessed by KdpB
GO:1903103 potassium:proton antiporter complex
IPI
PMID:28636601
Crystal structure of the potassium-importing KdpFABC membran...
MODIFY
Summary: Complex-membership claim mapped to the wrong complex term: GO:1903103 is a potassium:proton antiporter complex, whereas KdpFABC is a P-type K+-transporting ATPase.
Reason: The full text of PMID:28636601 describes ATP-coupled K+ import by a P-type ATPase complex and contains no antiport claim. The complex membership itself is correct; GO:0031004 potassium ion-transporting ATPase complex, whose definition names the E. coli KdpFABC complex, is the right term (already annotated to KdpB by IDA and IBA).
Supporting Evidence:
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.
PMID:28636601
the energy of ATP is harnessed by KdpB

Core Functions

Catalytic P-type ATPase subunit of KdpFABC: binds Mg-ATP, forms the Asp307 phosphoenzyme and hydrolyses ATP, coupling this to uphill K+ uptake through KdpA and K+ release from KdpB to the cytoplasm (contributing to the complex's P-type potassium transporter activity).

Supporting Evidence:
  • PMID:30478378
    While ATP hydrolysis is accomplished by the P-type ATPase subunit KdpB
  • PMID:34272288
    Our structures suggest a mechanism where ATP hydrolysis is coupled to K+ transfer between alternative sites in KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K+ to the cytoplasm.
  • file:ECOLI/kdpB/kdpB-uniprot.txt
    D->E,N,Q: Unable to form a phosphorylated intermediate and lacks ATPase activity.

References

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Suggested Questions for Experts

Q: Which kinase phosphorylates KdpB Ser162, under what conditions, and is it dephosphorylated when K+ limitation returns?

Q: Should GO represent KdpB as enabling GO:0008556 or as contributing to it, given that KdpA supplies the selectivity filter but KdpB supplies both energy coupling and the cytoplasmic release site?

Suggested Experiments

Experiment: Identify the Ser162 kinase by screening kinase deletion strains for loss of KdpB phosphorylation after return to high K+, and test S162A/S162D effects on growth during K+ upshift.

Type: genetic screen with phosphoproteomics

πŸ“š Additional Documentation

Notes

(kdpB-notes.md)

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