P1B-1-type Cu(+)-translocating efflux ATPase CopA2 (VPARA_21930, A0A0H2M2H3; EC 7.2.2.8) in Variovorax paradoxus strain TBEA6 is a 747-amino-acid eight-pass inner-membrane heavy-metal P-type ATPase (NCBIfam TIGR01511 ATPase-IB1_Cu, InterPro IPR027256, PANTHER PTHR43520:SF8, FunFam 2.70.150.10:FF:000020) encoded on genomic contig JZWI01000010 (EMBL KLN56614.1). CopA2 comprises an N-terminal cytoplasmic heavy-metal-associated (HMA) regulatory domain (PROSITE PS50846, Pfam PF00403, CDD cd00371, residues 13-80) housing the conserved Cu(+)-binding 22-MTCASCV-28 CXXC motif, eight RuleBase-annotated transmembrane alpha-helices (residues 98-116, 128-147, 159-181, 193-212, 349-371, 377-410, 700-719, and 725-742) with the intramembrane 390-CPCALGLATP-399 (Cys390-Pro391-Cys392) Cu(+) translocation site in TM6, a cytoplasmic actuator (A) domain (Pfam PF00122, with the 287-TGEP-290 phosphatase loop), and a haloacid dehalogenase (HAD)-like catalytic phosphorylation (P) and nucleotide-binding (N) domain (Pfam PF00702, PROSITE PS00154, InterPro IPR023299) containing the invariant acyl-phosphate acceptor Asp434 (within 434-DKTGTLT-440) and Mg(2+)-binding hinge (638-GDGVNDAPALA-648). CopA2 couples ATP hydrolysis to active export of monovalent copper (Cu(+)) across the bacterial plasma membrane into the periplasm to maintain cellular copper homeostasis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000166 nucleotide binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but uninformative parent molecular function already entailed by the accepted specific child term GO:0005524 (ATP binding). Reason: GO:0000166 (nucleotide binding) is a broad ancestor term that adds no specificity beyond GO:0005524 (ATP binding) already accepted in this review. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR InterPro; IPR023299; ATPase_P-typ_cyto_dom_N. |
| GO:0005507 copper ion binding | IEA GO_REF:0000118 | ACCEPT | Summary: Core substrate/regulatory metal-binding activity at the N-terminal HMA domain (PROSITE PS50846, residues 13-80, 22-MTCASCV-28) and intramembrane TM6 390-CPC-392 translocation site. Reason: CopA2 contains an N-terminal cytoplasmic HMA domain (PROSITE PS50846, Pfam PF00403, CDD cd00371, residues 13-80) with the canonical 22-MTCASCV-28 CXXC copper-binding motif and the TM6 390-CPCALGLATP-399 intramembrane copper-coordination site characteristic of P1B-1 Cu(+) ATPases (NCBIfam TIGR01511, PANTHER PTHR43520:SF8). Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt FT DOMAIN 13..80 FT /note="HMA" FT /evidence="ECO:0000259|PROSITE:PS50846" |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: Core cosubstrate-binding activity of the cytoplasmic P-type ATPase nucleotide-binding (N) and phosphorylation (P) domains (InterPro IPR023299, PROSITE PS00154). Reason: CopA2 contains a conserved P-type ATPase cytoplasmic nucleotide-binding domain (InterPro IPR023299) and E1-E2 phosphorylation site (PROSITE PS00154, 434-DKTGTLT-440) that bind ATP and form the transient Asp434 acyl-phosphate intermediate during Cu(+) export (matching VARPD/cadA2). Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR PROSITE; PS00154; ATPASE_E1_E2; 1. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Core subcellular localization of this eight-pass inner-membrane P1B-1 Cu(+)-exporting ATPase. Reason: CopA2 is a multi-pass integral inner-membrane P1B-1 ATPase (RuleBase RU362081) with eight transmembrane alpha-helices (residues 98-116, 128-147, 159-181, 193-212, 349-371, 377-410, 700-719, and 725-742) embedded in the bacterial plasma membrane. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt FT TRANSMEM 98..116 FT /note="Helical" FT /evidence="ECO:0000256|RuleBase:RU362081" |
| GO:0006812 monoatomic cation transport | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but uninformative parent biological process already entailed by the accepted specific child term GO:0060003 (copper ion export). Reason: GO:0006812 (monoatomic cation transport) is a broad ancestor term already entailed by GO:0060003 (copper ion export) accepted in this review. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR InterPro; IPR027256; P-typ_ATPase_IB. |
| GO:0015662 P-type ion transporter activity | IEA GO_REF:0000117 | TOO GENERAL | Summary: True but uninformative parent molecular function already entailed by the accepted specific child term GO:0140581 (P-type monovalent copper transporter activity). Reason: GO:0015662 (P-type ion transporter activity) is an ancestor of GO:0140581 (P-type monovalent copper transporter activity) already accepted in this review. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt CC -!- SIMILARITY: Belongs to the cation transport ATPase (P-type) (TC 3.A.3) CC family. Type IB subfamily. {ECO:0000256|ARBA:ARBA00006024, CC ECO:0000256|RuleBase:RU362081}. |
| GO:0016020 membrane | IEA GO_REF:0000120 | TOO GENERAL | Summary: True but uninformative parent cellular component already entailed by the accepted specific child term GO:0005886 (plasma membrane). Reason: GO:0016020 (membrane) adds no specificity beyond GO:0005886 (plasma membrane) already accepted in this review. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt FT TRANSMEM 98..116 FT /note="Helical" FT /evidence="ECO:0000256|RuleBase:RU362081" |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but uninformative parent molecular function already entailed by the accepted specific child term GO:0140581 (P-type monovalent copper transporter activity). Reason: GO:0016887 (ATP hydrolysis activity) is an is_a ancestor of GO:0140581 (P-type monovalent copper transporter activity) and adds no independent information (matching VARPD/cadA2). Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR PROSITE; PS00154; ATPASE_E1_E2; 1. |
| GO:0019829 ATPase-coupled monoatomic cation transmembrane transporter activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but uninformative parent molecular function already entailed by the accepted specific child term GO:0140581 (P-type monovalent copper transporter activity). Reason: GO:0019829 is an ancestor of GO:0140581 (P-type monovalent copper transporter activity) already accepted in this review. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR InterPro; IPR027256; P-typ_ATPase_IB. |
| GO:0043682 P-type divalent copper transporter activity | IEA GO_REF:0000118 | MODIFY | Summary: TreeGrafter oxidation-state error; P1B-1-subfamily CopA ATPases translocate monovalent Cu(+) (GO:0140581) rather than divalent Cu(2+). Reason: CopA2 belongs to the P1B-1 Cu(+)-ATPase subfamily (NCBIfam TIGR01511 ATPase-IB1_Cu, PANTHER PTHR43520:SF8 P-TYPE CU(+) TRANSPORTER, EC 7.2.2.8), which coordinates and exports monovalent Cu(+) from the reducing bacterial cytoplasm; refine laterally to GO:0140581 (P-type monovalent copper transporter activity), which is already accepted on this review. Proposed replacements: P-type monovalent copper transporter activity Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR NCBIfam; TIGR01511; ATPase-IB1_Cu; 1. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but uninformative parent molecular function already entailed by the accepted specific child term GO:0005507 (copper ion binding). Reason: GO:0046872 (metal ion binding) adds no specificity beyond GO:0005507 (copper ion binding) already accepted in this review. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt FT DOMAIN 13..80 FT /note="HMA" FT /evidence="ECO:0000259|PROSITE:PS50846" |
| GO:0046915 transition metal ion transmembrane transporter activity | IEA GO_REF:0000117 | TOO GENERAL | Summary: True but uninformative parent molecular function already entailed by the accepted specific child term GO:0140581 (P-type monovalent copper transporter activity). Reason: GO:0046915 is an ancestor of GO:0140581 (P-type monovalent copper transporter activity) already accepted in this review. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR NCBIfam; TIGR01511; ATPase-IB1_Cu; 1. |
| GO:0055070 copper ion homeostasis | IEA GO_REF:0000118 | ACCEPT | Summary: Core biological process; CopA2 exports excess cytoplasmic Cu(+) to maintain intracellular copper homeostasis. Reason: P1B-1 Cu(+)-exporting ATPases (NCBIfam TIGR01511, PANTHER PTHR43520:SF8, FunFam 2.70.150.10:FF:000020) are the primary inner-membrane efflux pumps responsible for bacterial cytoplasmic copper homeostasis and detoxification. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR FunFam; 2.70.150.10:FF:000020; Copper-exporting P-type ATPase A; 1. DR FunFam; 3.30.70.100:FF:000005; Copper-exporting P-type ATPase A; 1. |
| GO:0060003 copper ion export | IEA GO_REF:0000117 | ACCEPT | Summary: Core biological process; CopA2 catalyzes ATP-driven export of cytoplasmic Cu(+) across the inner membrane into the periplasm. Reason: In Gram-negative Proteobacteria, P1B-1 Cu(+)-ATPases (NCBIfam TIGR01511, PANTHER PTHR43520:SF8, FunFam Copper-exporting P-type ATPase A) export monovalent Cu(+) out of the cytoplasm into the periplasm. Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR FunFam; 2.70.150.10:FF:000020; Copper-exporting P-type ATPase A; 1. DR FunFam; 3.30.70.100:FF:000005; Copper-exporting P-type ATPase A; 1. |
| GO:0140581 P-type monovalent copper transporter activity | IEA GO_REF:0000003 | ACCEPT | Summary: Core molecular function (EC 7.2.2.8) coupling ATP hydrolysis at Asp434 to transmembrane translocation of monovalent Cu(+). Reason: CopA2 possesses the complete P1B-1 Cu(+)-translocating P-type ATPase machinery (NCBIfam TIGR01511, PANTHER PTHR43520:SF8, N-terminal HMA 22-MTCASCV-28, TM6 390-CPCALGLATP-399, TM7/8 Tyr706-Asn707 and Met736, and PROSITE PS00154 434-DKTGTLT-440 phosphorylation site; EC 7.2.2.8). Supporting Evidence: file:VARPD/copA2/copA2-uniprot.txt DR NCBIfam; TIGR01511; ATPase-IB1_Cu; 1. |
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Download this section (compressed HTML)Q: Does Variovorax paradoxus CopA2 (VPARA_21930) function primarily in bulk cytoplasmic Cu(+) detoxification under copper stress, or does it also deliver Cu(+) to periplasmic cuproenzymes such as cytochrome c oxidase?
Suggested experts: Arguello JM, Rensing C
Experiment: Construct a ΞcopA2 (VPARA_21930) deletion mutant in Variovorax paradoxus TBEA6 and compare CuSO4 and AgNO3 minimum inhibitory concentrations, intracellular copper accumulation by ICP-MS, and everted membrane vesicle ATP-dependent Cu(+) transport against wild type.
Hypothesis: Loss of copA2 causes intracellular copper hyperaccumulation and hypersensitivity to Cu(+) stress, whereas wild-type CopA2 catalyzes vanadate-sensitive, ATP-driven Cu(+) export across the inner membrane.
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