Cobalt-zinc-cadmium resistance protein CzcB (VPARA_44900) in Variovorax paradoxus strain TBEA6 is a 455-amino-acid periplasmic membrane-fusion protein (MFP) adaptor subunit (NCBIfam TIGR01730, InterPro IPR006143) that bridges the inner-membrane HME-RND cation-proton antiporter CzcA3 (VPARA_44890) and the outer-membrane factor channel CzcC (VPARA_44910) across the periplasmic space to assemble the tripartite CzcCBA heavy-metal efflux pump. Anchored to the inner membrane by an N-terminal transmembrane helix (residues 18-36), CzcB extends into the periplasm via a histidine- and carboxylate-rich disordered region (residues 41-121, containing 10 histidine residues) followed by four canonical CzcB/CusB adaptor domains β a barrel-sandwich hybrid domain (Pfam PF25973, residues 155-298) with an embedded alpha-helical hairpin (Pfam PF25893, residues 194-253), a CusB-like beta-barrel domain (Pfam PF25954, residues 301-376), and a C-terminal circularly permuted SH3-like domain (Pfam PF25975, residues 383-443) β that physically couple CzcA3 and CzcC during trans-envelope export of monoatomic metal cations.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0015679 plasma membrane copper ion transport | IEA GO_REF:0000118 | MODIFY | Summary: Overly specific TreeGrafter propagation from CusB copper-efflux homologs within PANTHER family PTHR30097; generalize to GO:0098655 (monoatomic cation transmembrane transport). Reason: PANTHER family PTHR30097 encompasses both monovalent-copper CusB and divalent-cation (Co2+/Zn2+/Cd2+) CzcB membrane-fusion proteins. VPARA_44900 carries CzcB-specific domain signatures (Pfam PF25973 BSH_CzcB, PF25893 HH_CzcB, PF25975 CzcB_C) and is encoded in the czcA3-czcB-czcC (VPARA_44890-VPARA_44910) operon, whose exact metal substrate specificity in Variovorax paradoxus has not been experimentally restricted to copper. Generalizing to GO:0098655 (monoatomic cation transmembrane transport) accurately reflects its conserved role in the tripartite CzcCBA cation efflux pump. Proposed replacements: monoatomic cation transmembrane transport Supporting Evidence: UniProtKB:A0A0H2LX82 DR NCBIfam; TIGR01730; RND_mfp; 1. PMID:10559151 The Czc system of Ralstonia sp. strain CH34 mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB(2)A cation-proton antiporter. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: Correct but overly general cellular component; refine to GO:0005886 (plasma membrane) to reflect the N-terminal inner-membrane anchor helix (residues 18-36). Reason: CzcB (VPARA_44900) is anchored to the bacterial inner (plasma) membrane via its N-terminal transmembrane alpha-helix (residues 18-36) while its adaptor domains extend into the periplasm. Proposed replacements: plasma membrane Supporting Evidence: UniProtKB:A0A0H2LX82 FT TRANSMEM 18..36 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO over-annotates the non-pore-forming periplasmic membrane-fusion adaptor CzcB with the transmembrane transporter activity of the assembled tripartite CzcCBA complex; CzcB itself enables structural molecule activity (GO:0005198) and contributes_to efflux transmembrane transporter activity (GO:0015562). Reason: In tripartite RND efflux pumps (CzcCBA), active cation-proton antiport is catalyzed by the inner-membrane RND subunit CzcA3 (VPARA_44890) and outer-membrane passage occurs through the trimeric OMF channel CzcC (VPARA_44910), whereas CzcB (VPARA_44900, InterPro IPR006143) is a periplasmic membrane-fusion adaptor that bridges CzcA3 and CzcC without forming a transmembrane pore itself. Asserting that CzcB independently enables transmembrane transporter activity (GO:0022857) over-annotates a non-transporting structural adaptor; instead, CzcB enables structural molecule activity (GO:0005198) and contributes_to efflux transmembrane transporter activity (GO:0015562) within the assembled CzcCBA complex. Supporting Evidence: UniProtKB:A0A0H2LX82 DR NCBIfam; TIGR01730; RND_mfp; 1. PMID:10559151 The Czc system of Ralstonia sp. strain CH34 mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB(2)A cation-proton antiporter. |
| GO:0030288 outer membrane-bounded periplasmic space | IEA GO_REF:0000118 | ACCEPT | Summary: Accurate core subcellular localization for the soluble ectodomain of CzcB; while anchored in the plasma membrane by residues 18-36, its four adaptor domains (residues 155-443) span the Gram-negative periplasmic space to link inner-membrane CzcA3 with outer-membrane CzcC. Reason: While CzcB is anchored to the plasma membrane (`GO:0005886`) via its N-terminal transmembrane helix (residues 18-36), the bulk of the protein β comprising the disordered region (residues 41-121) and four structural adaptor domains (residues 155-443) β resides in and spans the outer membrane-bounded periplasmic space to bridge CzcA3 and CzcC. Supporting Evidence: UniProtKB:A0A0H2LX82 FT DOMAIN 155..298 FT /note="CzcB-like barrel-sandwich hybrid" FT /evidence="ECO:0000259|Pfam:PF25973" |
| GO:0030313 cell envelope | IEA GO_REF:0000118 | TOO GENERAL | Summary: True but overly general parent term subsumed by the accepted GO:0030288 (outer membrane-bounded periplasmic space) and modified GO:0005886 (plasma membrane) annotations. Reason: GO:0030313 (cell envelope) is true of CzcB but uninformative because its more specific constituent compartments GO:0030288 (outer membrane-bounded periplasmic space) and GO:0005886 (plasma membrane) are already asserted on this review. Supporting Evidence: UniProtKB:A0A0H2LX82 FT DOMAIN 155..298 FT /note="CzcB-like barrel-sandwich hybrid" FT /evidence="ECO:0000259|Pfam:PF25973" |
| GO:0046914 transition metal ion binding | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: Auxiliary non-core molecular function inferred by TreeGrafter; CzcB possesses a histidine- and carboxylate-rich N-terminal periplasmic region (residues 41-121), but direct metal binding has not been biochemically assayed in Variovorax paradoxus and its primary role is as the structural periplasmic adaptor of the CzcCBA pump. Reason: TreeGrafter (PTN002409546) transfers GO:0046914 (transition metal ion binding) from characterized CusB/CzcB-family adaptors. While residues 41-121 of VPARA_44900 form a histidine- and carboxylate-rich periplasmic region (containing 10 histidine residues) consistent with auxiliary metal coordination in CzcB homologs, direct metal binding has not been experimentally assayed on VPARA_44900 and its core biological role is serving as the periplasmic structural adaptor of the CzcCBA efflux complex. Supporting Evidence: UniProtKB:A0A0H2LX82 FT COMPBIAS 45..121 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" PMID:10559151 The Czc system of Ralstonia sp. strain CH34 mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB(2)A cation-proton antiporter. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | MODIFY | Summary: Correct but overly general biological process; refine to GO:0098655 (monoatomic cation transmembrane transport). Reason: GO:0055085 (transmembrane transport) is a generic parent term; within the czcA3-czcB-czcC operon, CzcB specifically mediates monoatomic cation transmembrane transport (GO:0098655). Proposed replacements: monoatomic cation transmembrane transport Supporting Evidence: UniProtKB:A0A0H2LX82 DR NCBIfam; TIGR01730; RND_mfp; 1. PMID:10559151 The Czc system of Ralstonia sp. strain CH34 mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB(2)A cation-proton antiporter. |
| GO:0060003 copper ion export | IEA GO_REF:0000118 | MODIFY | Summary: Overly specific TreeGrafter propagation from CusB copper-efflux homologs in PANTHER PTHR30097; generalize to GO:0098655 (monoatomic cation transmembrane transport). Reason: TreeGrafter (PTN002409546) transfers copper ion export from CusB members of PTHR30097, whereas VPARA_44900 is a CzcB-subfamily adaptor (Pfam PF25973, PF25893, PF25975) in the czcA3-czcB-czcC heavy-metal cation efflux operon. Generalizing to GO:0098655 avoids asserting unverified copper-only specificity. Proposed replacements: monoatomic cation transmembrane transport Supporting Evidence: UniProtKB:A0A0H2LX82 FT DOMAIN 155..298 FT /note="CzcB-like barrel-sandwich hybrid" FT /evidence="ECO:0000259|Pfam:PF25973" PMID:10559151 The Czc system of Ralstonia sp. strain CH34 mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB(2)A cation-proton antiporter. |
| GO:0005198 structural molecule activity | ISS PMID:10559151 CzcD is a heavy metal ion transporter involved in regulation... | NEW | Summary: CzcB serves as the structural periplasmic membrane-fusion adaptor bridging the inner-membrane RND antiporter CzcA3 and the outer-membrane channel CzcC in the tripartite CzcCBA complex. Reason: Inferred from sequence and structural domain similarity (ISS) to bacterial RND membrane-fusion proteins (NCBIfam TIGR01730, Pfam PF25973, PMID:10559151; PMID:12829273), where CzcB forms the periplasmic structural adaptor linking the inner-membrane CzcA antiporter and outer-membrane CzcC channel without itself catalyzing transmembrane transport. Supporting Evidence: UniProtKB:A0A0H2LX82 FT DOMAIN 155..298 FT /note="CzcB-like barrel-sandwich hybrid" FT /evidence="ECO:0000259|Pfam:PF25973" PMID:10559151 The Czc system of Ralstonia sp. strain CH34 mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB(2)A cation-proton antiporter. |
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Download this section (compressed HTML)Q: Does the histidine-rich N-terminal periplasmic region (residues 41-121, containing 10 histidine residues) of Variovorax paradoxus CzcB (VPARA_44900) deliver periplasmic Zn2+/Co2+/Cd2+ ions directly to the CzcA3 porter domain or act as an allosteric metal sensor that activates the CzcCBA pump?
Suggested experts: Nies DH, Su CC, Yu EW
Experiment: Compare heavy-metal minimum inhibitory concentrations (Zn2+, Co2+, Cd2+, Ni2+, Cu2+) of wild-type Variovorax paradoxus TBEA6, a ΞczcB (VPARA_44900) deletion mutant, and a czcB variant lacking the histidine-rich periplasmic segment (Ξ45-121).
Hypothesis: Deletion of czcB abolishes CzcCBA-mediated divalent metal resistance, while truncation of the histidine-rich segment (residues 45-121) impairs allosteric activation or low-concentration periplasmic metal scavenging.
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