Cadmium, cobalt and zinc/H(+)-K(+) antiporter CzcD (VPARA_15480) in Variovorax paradoxus strain TBEA6 is a 320-amino-acid inner-membrane Cation Diffusion Facilitator (CDF) family transporter (NCBIfam TIGR01297, NCBIfam NF033827, Pfam PF01545, InterPro IPR002524) containing six Phobius-predicted transmembrane alpha-helices (residues 28-47, 59-80, 92-113, 125-148, 185-210, and 216-234; refining early hydropathy estimates of "at least four transmembrane alpha-helices", PMID:10559151), an extraordinarily histidine-rich cytoplasmic loop between TM4 and TM5 (residues 152-179, containing 15 histidine residues within 152-HHHGHGHDHGHGHAHPHHEGHGHAHGHD-179), and a C-terminal cytoplasmic regulatory domain (residues 243-320). CzcD preserves the conserved intramembrane metal-binding site A residues on TM2 (His59 and His62 in 59-HMSSHALA-66) and TM5 (His188 and Asp192 in 188-HVVAD-192) and catalyzes proton-coupled export of cytoplasmic Zn(2+) (as well as Co(2+) and Cd(2+)) across the plasma membrane to maintain intracellular zinc and transition-metal ion homeostasis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005385 zinc ion transmembrane transporter activity | IEA GO_REF:0000002 | ACCEPT | Summary: Accurate core molecular function of the CDF-family Zn(2+)/Co(2+)/Cd(2+) efflux antiporter CzcD. Reason: CzcD (VPARA_15480) belongs to the Cation Diffusion Facilitator (CDF) family (NCBIfam TIGR01297, Pfam PF01545, InterPro IPR002524) and retains the canonical TM2/TM5 intramembrane metal-binding site (His59, His62, His188, Asp192) and cytosolic histidine-rich loop (residues 152-179) that mediate transmembrane export of cytoplasmic zinc ions (as well as cobalt and cadmium ions). Supporting Evidence: UniProtKB:A0A0H2M558 FT DOMAIN 29..242 FT /note="Cation efflux protein transmembrane" FT /evidence="ECO:0000259|Pfam:PF01545" PMID:10559151 All three proteins mediated a small but significant resistance to cobalt, zinc, and cadmium in Ralstonia, and this resistance was based on a reduced accumulation of the cations. |
| GO:0006812 monoatomic cation transport | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but overly general parent term subsumed by the accepted GO:0071577 (zinc ion transmembrane transport) annotation. Reason: GO:0006812 (monoatomic cation transport) is true of CzcD but uninformative because the more specific descendant term GO:0071577 (zinc ion transmembrane transport) is already asserted on this review. Supporting Evidence: UniProtKB:A0A0H2M558 DR NCBIfam; TIGR01297; CDF; 1. |
| GO:0006829 zinc ion transport | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but overly general parent term subsumed by the accepted GO:0071577 (zinc ion transmembrane transport) annotation. Reason: GO:0006829 (zinc ion transport) is true of CzcD but subsumed by its more specific child term GO:0071577 (zinc ion transmembrane transport) already accepted on this record. Supporting Evidence: UniProtKB:A0A0H2M558 DR NCBIfam; TIGR01297; CDF; 1. |
| GO:0006882 intracellular zinc ion homeostasis | IEA GO_REF:0000002 | ACCEPT | Summary: Accurate core biological process; CzcD exports excess cytoplasmic Zn(2+) to maintain intracellular zinc homeostasis and attenuate CzcCBA induction. Reason: Bacterial CzcD CDF transporters export excess cytoplasmic Zn(2+) across the inner membrane to prevent toxic intracellular zinc accumulation and regulate heavy-metal resistance homeostasis. Supporting Evidence: PMID:10559151 All three proteins mediated a small but significant resistance to cobalt, zinc, and cadmium in Ralstonia, and this resistance was based on a reduced accumulation of the cations. Thus, CzcD appeared to repress the Czc system by an export of the inducing cations. PMID:27797207 We identified dozens of proteins that responded to zinc in a ColR-independent manner, among others, known metal efflux systems CzcCBA1, CzcCBA2, CadA2 and CzcD. |
| GO:0008324 monoatomic cation transmembrane transporter activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but overly general parent term subsumed by the accepted GO:0005385 (zinc ion transmembrane transporter activity) annotation. Reason: GO:0008324 (monoatomic cation transmembrane transporter activity) is true of CzcD but subsumed by the more specific accepted child term GO:0005385 (zinc ion transmembrane transporter activity). Supporting Evidence: UniProtKB:A0A0H2M558 DR NCBIfam; TIGR01297; CDF; 1. |
| GO:0016020 membrane | IEA GO_REF:0000120 | MODIFY | Summary: Correct but overly general cellular component; refine to GO:0005886 (plasma membrane) to reflect the six inner-membrane transmembrane helices of CzcD. Reason: CzcD (VPARA_15480) is an integral inner-membrane protein with six transmembrane alpha-helices (residues 28-47, 59-80, 92-113, 125-148, 185-210, and 216-234) localized to the bacterial plasma membrane (GO:0005886). Proposed replacements: plasma membrane Supporting Evidence: UniProtKB:A0A0H2M558 FT TRANSMEM 28..47 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" PMID:10559151 The CzcD protein is involved in the regulation of the Czc system. It is a membrane-bound protein with at least four transmembrane alpha-helices and is a member of a subfamily of the cation diffusion facilitator (CDF) protein family, which occurs in all three domains of life. |
| GO:0030001 metal ion transport | IEA GO_REF:0000118 | TOO GENERAL | Summary: True but overly general parent term subsumed by the accepted GO:0071577 (zinc ion transmembrane transport) annotation. Reason: GO:0030001 (metal ion transport) is true of CzcD but uninformative because the more specific descendant term GO:0071577 (zinc ion transmembrane transport) is already accepted on this review. Supporting Evidence: UniProtKB:A0A0H2M558 DR NCBIfam; TIGR01297; CDF; 1. |
| GO:0046873 metal ion transmembrane transporter activity | IEA GO_REF:0000118 | TOO GENERAL | Summary: True but overly general parent term subsumed by the accepted GO:0005385 (zinc ion transmembrane transporter activity) annotation. Reason: GO:0046873 (metal ion transmembrane transporter activity) is true of CzcD but subsumed by its accepted child term GO:0005385 (zinc ion transmembrane transporter activity). Supporting Evidence: UniProtKB:A0A0H2M558 DR NCBIfam; TIGR01297; CDF; 1. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but overly general parent term subsumed by the accepted GO:0071577 (zinc ion transmembrane transport) annotation. Reason: GO:0055085 (transmembrane transport) is true of CzcD but uninformative because the specific descendant term GO:0071577 (zinc ion transmembrane transport) is already accepted on this review. Supporting Evidence: UniProtKB:A0A0H2M558 DR NCBIfam; TIGR01297; CDF; 1. |
| GO:0071577 zinc ion transmembrane transport | IEA GO_REF:0000108 | ACCEPT | Summary: Accurate core biological process of the inner-membrane CDF zinc/divalent cation efflux antiporter CzcD. Reason: CzcD mediates proton-coupled transmembrane export of cytoplasmic zinc ions (as well as cobalt and cadmium ions) across the bacterial inner membrane. Supporting Evidence: UniProtKB:A0A0H2M558 FT DOMAIN 29..242 FT /note="Cation efflux protein transmembrane" FT /evidence="ECO:0000259|Pfam:PF01545" PMID:10559151 All three proteins mediated a small but significant resistance to cobalt, zinc, and cadmium in Ralstonia, and this resistance was based on a reduced accumulation of the cations. |
| GO:0098655 monoatomic cation transmembrane transport | IEA GO_REF:0000108 | TOO GENERAL | Summary: True but overly general parent term subsumed by the accepted GO:0071577 (zinc ion transmembrane transport) annotation. Reason: GO:0098655 (monoatomic cation transmembrane transport) is true of CzcD but subsumed by its accepted child term GO:0071577 (zinc ion transmembrane transport). Supporting Evidence: UniProtKB:A0A0H2M558 DR NCBIfam; TIGR01297; CDF; 1. |
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Download this section (compressed HTML)Q: What is the functional role of the unusually long 28-residue histidine-rich cytosolic IL2 loop (152-HHHGHGHDHGHGHAHPHHEGHGHAHGHD-179, containing 15 histidines) in Variovorax paradoxus CzcD (VPARA_15480) β does it act as an intracellular Zn2+/Ni2+/Co2+ buffer or an allosteric gate for transmembrane transport?
Suggested experts: Nies DH, Barber KE, Cherezov V
Experiment: Reconstitute purified Variovorax paradoxus CzcD (VPARA_15480) and an IL2 histidine-loop deletion variant (Ξ152-179) into proteoliposomes and measure ΞpH-driven transport of Zn2+, Co2+, Cd2+, and Ni2+.
Hypothesis: Wild-type CzcD catalyzes H+-coupled antiport of Zn2+, Co2+, and Cd2+, while deletion of the 15-histidine cytoplasmic loop alters metal selectivity and allosteric activation kinetics.
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