P1B-type Zn(2+)/Cd(2+)-translocating efflux ATPase CadA2 (VPARA_44980, A0A0H2LVW9; EC 7.2.2.12, RHEA:20621) in Variovorax paradoxus strain TBEA6 is a 759-amino-acid multi-pass inner-membrane heavy-metal P-type ATPase (NCBIfam TIGR01512 ATPase-IB2_Cd, NCBIfam TIGR01525 ATPase-IB_hvy, InterPro IPR027256, PANTHER PTHR48085:SF5) encoded on genomic contig JZWI01000024 (EMBL KLN54354.1) within the same heavy-metal resistance island as the czcA3-czcB-czcC-czcI-czcR-cusS (VPARA_44890-VPARA_44940, KLN54345.1-KLN54350.1) cluster. CadA2 comprises an N-terminal cytoplasmic heavy-metal-associated (HMA) regulatory domain (CDD cd00371, InterPro IPR006121, containing the cysteine-rich 26-CCGSTAC-32 and 57-MDC-59 motifs), six RuleBase-annotated transmembrane alpha-helices (residues 140-160, 166-186, 198-214, 368-390, 705-726, and 732-750) plus the intramembrane metal-translocation segment carrying the canonical Cys410-Pro411-Cys412 (410-CPC-412) motif, a cytoplasmic actuator (A) domain (Pfam PF00122, residues 251-352, with the 296-TGES-299 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 Asp454 (within 454-DKTGTIT-460) and Mg(2+)-binding hinge (650-GDGINDAPALA-660). It couples ATP hydrolysis to active export of cytoplasmic Zn(2+) and Cd(2+) across the plasma membrane into the periplasm.
| 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/cadA2/cadA2-uniprot.txt DR InterPro; IPR023299; ATPase_P-typ_cyto_dom_N. |
| 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, IPR001757, PROSITE PS00154). Reason: CadA2 contains a conserved P-type ATPase cytoplasmic nucleotide-binding domain (InterPro IPR023299) and E1-E2 ATPase phosphorylation site (PROSITE PS00154, 454-DKTGTIT-460) that bind ATP and form the transient Asp454 acyl-phosphate intermediate during metal-cation export. Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR InterPro; IPR023299; ATPase_P-typ_cyto_dom_N. file:VARPD/cadA2/cadA2-uniprot.txt DR PROSITE; PS00154; ATPASE_E1_E2; 1. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Core subcellular localization of this multi-pass inner-membrane P1B-type heavy-metal efflux ATPase. Reason: CadA2 is a multi-pass integral inner-membrane P1B-type ATPase (RuleBase RU362081, InterPro IPR023298) with six annotated transmembrane helices (residues 140-160, 166-186, 198-214, 368-390, 705-726, and 732-750) plus the intramembrane 410-CPC-412 metal-translocation segment embedded in the bacterial plasma membrane. Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|RuleBase:RU362081}. |
| GO:0006812 monoatomic cation transport | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but uninformative parent process already entailed by the accepted specific child terms GO:0071577 (zinc ion transmembrane transport) and GO:0070574 (cadmium ion transmembrane transport). Reason: GO:0006812 (monoatomic cation transport) is a broad ancestor term already entailed by GO:0071577 (zinc ion transmembrane transport) and GO:0070574 (cadmium ion transmembrane transport) accepted in this review. Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR InterPro; IPR027256; P-typ_ATPase_IB. |
| GO:0015086 cadmium ion transmembrane transporter activity | IEA GO_REF:0000118 | ACCEPT | Summary: Core molecular function of P1B-2-subfamily CadA/ZntA heavy-metal efflux ATPases (NCBIfam TIGR01512, PANTHER PTHR48085:SF5). Reason: CadA2 belongs to the P1B-2 subfamily of soft-metal-transporting P-type ATPases (NCBIfam TIGR01512 ATPase-IB2_Cd, PANTHER PTHR48085:SF5), which catalyze ATP-dependent transmembrane export of both Cd(2+) and Zn(2+) across the bacterial inner membrane (PMID:9405611, PMID:12867443). Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR NCBIfam; TIGR01512; ATPase-IB2_Cd; 1. PMID:9405611 Everted membrane vesicles from a wild-type strain accumulated 65Zn(II) and 109Cd(II) by using ATP as an energy source. Transport was sensitive to vanadate, an inhibitor of P-type ATPases. PMID:12867443 Cadmium and zinc are removed from cells of Ralstonia metallidurans by the CzcCBA efflux pump and by two soft-metal-transporting P-type ATPases, CadA and ZntA. |
| 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) is true of CadA2 but adds no specificity beyond GO:0005886 (plasma membrane) already accepted in this review. Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|RuleBase:RU362081}. |
| GO:0016463 P-type zinc transporter activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core catalytic and transport activity (EC 7.2.2.12, RHEA:20621) coupling ATP hydrolysis to active transmembrane Zn(2+) export. Reason: CadA2 possesses the complete P1B-2 Zn(2+)/Cd(2+)-translocating P-type ATPase architecture (NCBIfam TIGR01512, PANTHER PTHR48085:SF5, PROSITE PS00154 454-DKTGTIT-460, intramembrane 410-CPC-412 site, EC 7.2.2.12, RHEA:20621) that couples ATP hydrolysis to cytoplasmic Zn(2+) export (PMID:9405611, PMID:12867443). Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR PANTHER; PTHR48085:SF5; CADMIUM_ZINC-TRANSPORTING ATPASE HMA4-RELATED; 1. PMID:9405611 Everted membrane vesicles from a wild-type strain accumulated 65Zn(II) and 109Cd(II) by using ATP as an energy source. Transport was sensitive to vanadate, an inhibitor of P-type ATPases. |
| 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:0016463 (P-type zinc transporter activity). Reason: GO:0016887 (ATP hydrolysis activity) is an is_a ancestor of GO:0016463 (P-type zinc transporter activity) and adds no independent information. Supporting Evidence: file:VARPD/cadA2/cadA2-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:0016463 (P-type zinc transporter activity). Reason: GO:0019829 is the direct parent of GO:0016463 (P-type zinc transporter activity), which is already accepted in this review. Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR InterPro; IPR027256; P-typ_ATPase_IB. |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000118 | TOO GENERAL | Summary: True but uninformative parent molecular function already entailed by GO:0016463 (P-type zinc transporter activity) and GO:0015086 (cadmium ion transmembrane transporter activity). Reason: GO:0022857 (transmembrane transporter activity) is a high-level ancestor term already entailed by the accepted specific child terms GO:0016463 and GO:0015086. Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR PANTHER; PTHR48085:SF5; CADMIUM_ZINC-TRANSPORTING ATPASE HMA4-RELATED; 1. |
| GO:0030001 metal ion transport | IEA GO_REF:0000120 | TOO GENERAL | Summary: True but uninformative parent biological process already entailed by GO:0071577 (zinc ion transmembrane transport) and GO:0070574 (cadmium ion transmembrane transport). Reason: GO:0030001 (metal ion transport) is an ancestor of GO:0071577 and GO:0070574, both of which are accepted in this review. Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR PANTHER; PTHR48085:SF5; CADMIUM_ZINC-TRANSPORTING ATPASE HMA4-RELATED; 1. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | MODIFY | Summary: Correct but general molecular function; refine to GO:0008270 (zinc ion binding) and GO:0046870 (cadmium ion binding) for the N-terminal HMA regulatory domain (CDD cd00371, InterPro IPR006121, 26-CCGSTAC-32) and intramembrane 410-CPC-412 coordination site. Reason: CadA2 contains an N-terminal cytoplasmic heavy-metal-associated (HMA) domain (CDD cd00371, InterPro IPR006121, SUPFAM SSF55008) with conserved cysteine metal-binding motifs (26-CCGSTAC-32 and 57-MDC-59) as well as the intramembrane 410-CPC-412 translocation site that directly coordinate Zn(2+) and Cd(2+) in P1B-2-subfamily CadA/ZntA ATPases (NCBIfam TIGR01512, PANTHER PTHR48085:SF5; PMID:9405611, PMID:12867443); refine GO:0046872 to both specific descendants GO:0008270 (zinc ion binding) and GO:0046870 (cadmium ion binding). Proposed replacements: zinc ion binding cadmium ion binding Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR InterPro; IPR006121; HMA_dom. file:VARPD/cadA2/cadA2-uniprot.txt DR NCBIfam; TIGR01512; ATPase-IB2_Cd; 1. PMID:9405611 Everted membrane vesicles from a wild-type strain accumulated 65Zn(II) and 109Cd(II) by using ATP as an energy source. Transport was sensitive to vanadate, an inhibitor of P-type ATPases. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000118 | TOO GENERAL | Summary: True but uninformative parent biological process already entailed by GO:0071577 (zinc ion transmembrane transport) and GO:0070574 (cadmium ion transmembrane transport). Reason: GO:0055085 (transmembrane transport) is a broad ancestor term already entailed by the accepted child terms GO:0071577 and GO:0070574. Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR PANTHER; PTHR48085:SF5; CADMIUM_ZINC-TRANSPORTING ATPASE HMA4-RELATED; 1. |
| GO:0070574 cadmium ion transmembrane transport | IEA GO_REF:0000108 | ACCEPT | Summary: Core biological process mediated by CadA2 (NCBIfam TIGR01512, PANTHER PTHR48085:SF5). Reason: P1B-2-type CadA/ZntA ATPases export cytoplasmic Cd(2+) across the inner membrane into the periplasm to confer cadmium resistance in synergy with the CzcCBA RND efflux complex (PMID:9405611, PMID:12867443). Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR NCBIfam; TIGR01512; ATPase-IB2_Cd; 1. PMID:12867443 Cadmium and zinc are removed from cells of Ralstonia metallidurans by the CzcCBA efflux pump and by two soft-metal-transporting P-type ATPases, CadA and ZntA. |
| GO:0071577 zinc ion transmembrane transport | IEA GO_REF:0000108 | ACCEPT | Summary: Core biological process mediated by CadA2 (EC 7.2.2.12, RHEA:20621, PANTHER PTHR48085:SF5). Reason: CadA2 catalyzes ATP-driven transmembrane export of cytoplasmic Zn(2+) across the bacterial inner membrane to maintain intracellular zinc homeostasis and prevent zinc toxicity (PMID:9405611, PMID:12867443). Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR PANTHER; PTHR48085:SF5; CADMIUM_ZINC-TRANSPORTING ATPASE HMA4-RELATED; 1. PMID:9405611 Everted membrane vesicles from a wild-type strain accumulated 65Zn(II) and 109Cd(II) by using ATP as an energy source. Transport was sensitive to vanadate, an inhibitor of P-type ATPases. |
| GO:0098655 monoatomic cation transmembrane transport | IEA GO_REF:0000108 | TOO GENERAL | Summary: True but uninformative parent biological process already entailed by GO:0071577 (zinc ion transmembrane transport) and GO:0070574 (cadmium ion transmembrane transport). Reason: GO:0098655 (monoatomic cation transmembrane transport) is an ancestor of both GO:0071577 and GO:0070574, which are already accepted in this review. Supporting Evidence: file:VARPD/cadA2/cadA2-uniprot.txt DR InterPro; IPR027256; P-typ_ATPase_IB. |
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Download this section (compressed HTML)Q: Does Variovorax paradoxus CadA2 (VPARA_44980) also translocate Pb(2+) in addition to Cd(2+) and Zn(2+), and how is its cytoplasmic-to-periplasmic efflux coordinated with trans-envelope extrusion by the adjacent CzcCBA (VPARA_44890-VPARA_44910) RND pump on contig JZWI01000024?
Suggested experts: Rensing C, Nies DH, Arguello JM
Experiment: Prepare everted membrane vesicles from wild-type and ΞcadA2 (VPARA_44980) Variovorax paradoxus TBEA6 strains and measure vanadate-sensitive, ATP-dependent transport of 65Zn(2+) and 109Cd(2+), alongside single and double deletion phenotypes with ΞczcA3 (VPARA_44890).
Hypothesis: CadA2 catalyzes ATP-driven cytoplasmic export of Cd(2+) and Zn(2+) into the periplasm, acting synergistically with CzcCBA to confer high-level cadmium and zinc resistance.
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