atpD

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005515 protein binding	IPI PMID:15690043 Interaction network containing conserved and essential prote...	REMOVE	Summary: High-throughput affinity purification of E. coli complexes recovered AtpD with AtpA. Reason: Generic protein binding is uninformative. The partner is the alpha subunit AtpA (P0ABB0), with which beta alternates in the alpha3beta3 hexamer; that relationship is captured by membership of the ATP synthase complex (GO:0045259) and by the complex activity GO:0046933, both accepted here. No more informative molecular function term describes a subunit-subunit contact within a complex. Removing the row does not mean the interaction is false. Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3.
GO:0005515 protein binding	IPI PMID:16079137 Protein complexes of the Escherichia coli cell envelope.	REMOVE	Summary: Cell-envelope complex survey recovered AtpD with AtpA. Reason: Generic protein binding is uninformative. The partner is the alpha subunit AtpA (P0ABB0), with which beta alternates in the alpha3beta3 hexamer; that relationship is captured by membership of the ATP synthase complex (GO:0045259) and by the complex activity GO:0046933, both accepted here. No more informative molecular function term describes a subunit-subunit contact within a complex. Removing the row does not mean the interaction is false. Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3.
GO:0005515 protein binding	IPI PMID:16606699 Large-scale identification of protein-protein interaction of...	REMOVE	Summary: Large-scale tagged-protein pull-down screen recovered AtpD with AtpA. Reason: Generic protein binding is uninformative. The partner is the alpha subunit AtpA (P0ABB0), with which beta alternates in the alpha3beta3 hexamer; that relationship is captured by membership of the ATP synthase complex (GO:0045259) and by the complex activity GO:0046933, both accepted here. No more informative molecular function term describes a subunit-subunit contact within a complex. Removing the row does not mean the interaction is false. Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3.
GO:0005515 protein binding	IPI PMID:16858726 A complexomic study of Escherichia coli using two-dimensiona...	REMOVE	Summary: Blue native/SDS-PAGE complexome study found AtpD in the same complex as AtpA. Reason: Generic protein binding is uninformative. The partner is the alpha subunit AtpA (P0ABB0), with which beta alternates in the alpha3beta3 hexamer; that relationship is captured by membership of the ATP synthase complex (GO:0045259) and by the complex activity GO:0046933, both accepted here. No more informative molecular function term describes a subunit-subunit contact within a complex. Removing the row does not mean the interaction is false. Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3.
GO:0005515 protein binding	IPI PMID:17137328 Systematic identification of the subproteome of Escherichia ...	REMOVE	Summary: Cell-envelope subproteome study found AtpD with AtpA. Reason: Generic protein binding is uninformative. The partner is the alpha subunit AtpA (P0ABB0), with which beta alternates in the alpha3beta3 hexamer; that relationship is captured by membership of the ATP synthase complex (GO:0045259) and by the complex activity GO:0046933, both accepted here. No more informative molecular function term describes a subunit-subunit contact within a complex. Removing the row does not mean the interaction is false. Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3.
GO:0005515 protein binding	IPI PMID:21602818 Structure of the ATP synthase catalytic complex (F(1)) from ...	REMOVE	Summary: The crystal structure of E. coli F1 shows beta packed against alpha in the alpha3beta3 ring. Reason: Generic protein binding is uninformative. The partner is the alpha subunit AtpA (P0ABB0), with which beta alternates in the alpha3beta3 hexamer; that relationship is captured by membership of the ATP synthase complex (GO:0045259) and by the complex activity GO:0046933, both accepted here. No more informative molecular function term describes a subunit-subunit contact within a complex. Removing the row does not mean the interaction is false. Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3.
GO:0005515 protein binding	IPI PMID:24561554 The binary protein-protein interaction landscape of Escheric...	REMOVE	Summary: Binary yeast two-hybrid screen of E. coli proteins reported AtpD-AtpA. Reason: Generic protein binding is uninformative. The partner is the alpha subunit AtpA (P0ABB0), with which beta alternates in the alpha3beta3 hexamer; that relationship is captured by membership of the ATP synthase complex (GO:0045259) and by the complex activity GO:0046933, both accepted here. No more informative molecular function term describes a subunit-subunit contact within a complex. Removing the row does not mean the interaction is false. Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3.
GO:0005524 ATP binding	IEA GO_REF:0000120	ACCEPT	Summary: Walker A motif GGAGVGKT (UniProt 150-157); beta binds Mg-nucleotide at the catalytic sites. Reason: Nucleotide binding at the catalytic site is a direct property of beta. Replacing the Walker A threonine (Thr156, literature numbering) impairs ATPase activity (PMID:1832155), its hydroxyl being essential for catalysis, and uncD mutations change the affinity of the first catalytic site for ATP (PMID:2859284). Supporting Evidence: PMID:1832155 a beta Thr156----Ala or Cys mutation impaired ATPase activity, suggesting that the hydroxyl moiety at position 156 is essential for the catalytic activity PMID:2859284 Both mutant enzymes showed reduced affinity for ATP at the first catalytic site.
GO:0005886 plasma membrane	IEA GO_REF:0000120	ACCEPT	Summary: Beta is a peripheral protein on the cytoplasmic face of the inner (plasma) membrane, as part of F1. Reason: Correct location; F1 is attached to the membrane Fo sector by the central and peripheral stalks. Supporting Evidence: file:ECOLI/atpD/atpD-uniprot.txt SUBCELLULAR LOCATION: Cell inner membrane; Peripheral membrane protein.
GO:0005886 plasma membrane	NAS PMID:10358096 A novel labeling approach supports the five-transmembrane mo...	ACCEPT	Summary: The paper maps the topology of Fo subunit a in the inner membrane; the location of beta follows from its being part of the membrane-bound F1Fo enzyme. Reason: The cited paper concerns subunit a, and the statement for beta is author-level (NAS). The location itself is correct and supported independently, so the row is kept. Supporting Evidence: file:ECOLI/atpD/atpD-uniprot.txt SUBCELLULAR LOCATION: Cell inner membrane; Peripheral membrane protein.
GO:0015986 proton motive force-driven ATP synthesis	IEA GO_REF:0000120	MODIFY	Summary: Beta catalyses PMF-driven ATP synthesis by the F1Fo complex. Reason: Correct but general. In E. coli this happens at the plasma (inner) membrane, so the specific child GO:0042777 applies; the gene already carries it by IMP. Proposed replacements: proton motive force-driven plasma membrane ATP synthesis Supporting Evidence: file:ECOLI/atpD/atpD-uniprot.txt Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3.
GO:0016020 membrane	HDA PMID:16858726 A complexomic study of Escherichia coli using two-dimensiona...	MODIFY	Summary: Blue native/SDS-PAGE of membrane complexes recovered AtpD. Reason: Correct but general: the membrane in question is the inner (plasma) membrane, which the gene already carries (GO:0005886). Proposed replacements: plasma membrane Supporting Evidence: file:ECOLI/atpD/atpD-uniprot.txt SUBCELLULAR LOCATION: Cell inner membrane; Peripheral membrane protein.
GO:0016020 membrane	IEA GO_REF:0000117	MODIFY	Summary: ARBA-derived membrane annotation. Reason: Correct but general; the specific location is the plasma (inner) membrane (GO:0005886), which the gene already carries. Proposed replacements: plasma membrane Supporting Evidence: file:ECOLI/atpD/atpD-uniprot.txt SUBCELLULAR LOCATION: Cell inner membrane; Peripheral membrane protein.
GO:0042777 proton motive force-driven plasma membrane ATP synthesis	IMP PMID:2874137 Impaired proton conductivity resulting from mutations in the...	ACCEPT	Summary: Genetic analysis of the E. coli F1Fo ATPase, measuring ATP-driven membrane energization and F1 binding in uncB (subunit a) mutants. Reason: The cached abstract concerns subunit a mutants; the curator may have used other data in the full text. The term is the precise process for beta: ATP synthesis at the plasma membrane driven by the PMF, which beta catalyses. Beta mutants are uncoupled and lose oxidative phosphorylation (PMID:158358). Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3. PMID:158358 Five uncoupled mutant strains of Escherichia coli carrying mutations in the uncD gene have been studied.
GO:0045259 proton-transporting ATP synthase complex	IBA GO_REF:0000033	ACCEPT	Summary: IBA from the PTHR15184 duplication node PTN008558586. Reason: Correct for beta. The PTHR15184 family review judges the IBD node too deep because it also covers the type III export ATPases, but E. coli AtpD sits in the F1-beta clade (PTN008558588), where the term is right. AtpD is itself one of the seeds. Supporting Evidence: PMID:28001127 The Fo motor spans the membrane converting the potential energy of the proton motive force (pmf) into rotation of the central stalk that in turn drives conformational changes in the F1 catalytic sites.
GO:0045259 proton-transporting ATP synthase complex	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO mapping from the F1 beta subunit family (IPR005722). Reason: Beta is a core subunit of the F1Fo ATP synthase. Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3.
GO:0045259 proton-transporting ATP synthase complex	IPI PMID:28001127 Cryo-EM structures of the autoinhibited E. coli ATP synthase...	ACCEPT	Summary: Cryo-EM structures of intact E. coli F1Fo in three rotational states include the three beta subunits. Reason: Direct structural evidence that beta is part of the assembled complex. Supporting Evidence: PMID:28001127 These different catalytic states relate to the position of the curved coiled-coil of subunit γ in the central stalk, which drives the conformational changes associated with catalysis.
GO:0046034 ATP metabolic process	IEA GO_REF:0000002	TOO GENERAL	Summary: InterPro2GO mapping from the alpha/beta ATPase N-terminal domain. Reason: True but uninformative beside GO:0042777 proton motive force-driven plasma membrane ATP synthesis, which the gene carries and which entails it. Supporting Evidence: file:ECOLI/atpD/atpD-uniprot.txt Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits.
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism	IBA GO_REF:0000033	ACCEPT	Summary: IBA (contributes_to) from PTN008558586; AtpD is one of the seeds. Reason: The core activity, to which beta contributes the catalytic sites. As for the complex term, the node is too deep only for the type III export ATPases; AtpD is in the F1-beta clade. AtpD appearing among its own sources is expected. Supporting Evidence: PMID:21602818 Subunit γ forms the main, asymmetric shaft of F1’s rotor, and transport-driven rotation of γ relative to the surrounding α3β3 complex of F1 drives alternating conformational changes in the three catalytic β subunits to drive net synthesis of ATP1–3. PMID:7479919 The results demonstrate that gamma subunit rotates relative to the beta subunits during catalysis.
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism	IDA PMID:2863270 Assembly of a functional F1 of the proton-translocating ATPa...	ACCEPT	Summary: In vivo assembly study: beta (uncD) mutations prevent assembly of the alpha3beta3gamma F1 core, and assembled F1 restores energy-linked functions to F1-depleted membranes. Reason: Supports the contribution of beta to the complex activity (contributes_to). Supporting Evidence: PMID:2863270 Mutations of the uncA(alpha), uncG(gamma), or uncD(beta) genes result in a defective assembly of the F1 complex.
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism	IEA GO_REF:0000120	ACCEPT	Summary: Electronic annotation from the HAMAP rule and IPR005722. Reason: Core activity of the complex, with beta carrying the catalytic sites. Supporting Evidence: file:ECOLI/atpD/atpD-uniprot.txt Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits.
GO:0046961 proton-transporting ATPase activity, rotational mechanism	IMP PMID:158358 Properties of membranes from mutant strains of Escherichia c...	KEEP AS NON CORE	Summary: uncD mutant membranes lack ATPase activity (four of five alleles) and are uncoupled. The F1Fo complex can run in reverse, hydrolysing ATP to pump protons when the PMF is low. Reason: A real, retained capacity of the complex, used in E. coli when respiration is not available, but the reverse of the main physiological direction. Consistent with the PTHR15184 family review, which treats ATP hydrolysis as a retained non-core F-type capacity. Supporting Evidence: PMID:158358 ATPase activity was absent in the other four strains and the abnormal beta-subunits were tightly bound to the membranes. PMID:21602818 Rotational coupling is reversible and, if PMF drops below the energetic threshold needed to drive ATP synthesis, net ATP hydrolysis by the alternating catalytic sites on F1 can drive reverse rotation of γ and the c–ring of FO, thus pumping protons across the membrane in the opposite direction.
GO:1902600 proton transmembrane transport	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: InterPro2GO mapping from the alpha/beta ATPase N-terminal domain. Reason: Protons cross through Fo (subunits a and c); beta takes part only through rotary coupling. True at complex level, not the core contribution of beta. Supporting Evidence: PMID:21602818 Rotational coupling is reversible and, if PMF drops below the energetic threshold needed to drive ATP synthesis, net ATP hydrolysis by the alternating catalytic sites on F1 can drive reverse rotation of γ and the c–ring of FO, thus pumping protons across the membrane in the opposite direction.

Gene Description

Existing Annotations Review

Core Functions

Catalytic subunit of the F1 sector of the inner-membrane F1Fo ATP synthase. Beta carries the catalytic nucleotide sites of the alpha3beta3 hexamer; gamma rotation driven by proton flow through Fo cycles the three beta subunits through the binding-change states to make ATP from ADP and phosphate.

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