VPARA_00790

UniProt ID: A0A0H2MDH4
Organism: Variovorax paradoxus
Review Status: COMPLETE
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Gene Description

VPARA_00790 (A0A0H2MDH4) in Variovorax paradoxus is a 608-amino-acid periplasmic pyrroloquinoline quinone (PQQ)-dependent methanol/alcohol dehydrogenase [cytochrome c] subunit (EC 1.1.2.7; NCBIfam TIGR03075, InterPro IPR017512, Pfam PF01011, CDD cd10278) containing a cleavable 28-residue N-terminal Sec signal peptide (residues 1-28) and a soluble mature eight-bladed beta-propeller quinoprotein catalytic chain (residues 29-608) with a conserved vicinal disulfide bond (Cys130-Cys131). The active site coordinates a PQQ prosthetic group (via Glu83, Arg136, Thr180, and Thr266) and a catalytic Lewis-acid metal ion (via Glu198, Asn286, and Asp328) to oxidize primary alcohols in the periplasm and transfer electrons to a periplasmic cytochrome c acceptor. Notably, the active-site loop of VPARA_00790 (323-PYDEWDFDGIN-333) carries the Asp328-Phe329-Asp330 (Asp-X-Asp) motif whose second aspartate (Asp330) is characteristic of lanthanide/rare-earth-element (REE)-dependent XoxF-type quinoprotein dehydrogenases, making its physiological metal cofactor selectivity (Ca(2+) versus trivalent lanthanides) an open experimental question.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005509 calcium ion binding
IEA
GO_REF:0000002 		MODIFY
Reason: InterPro IPR017512 (PQQ_MeOH/EtOH_DH) and PIRSR617512-3 automatically map all members of the family to calcium ion binding (GO:0005509) at residues 198, 286, and 328. However, VPARA_00790 (A0A0H2MDH4) carries the Asp328-Phe329-Asp330 active-site motif containing the second aspartate (Asp330) that Keltjens et al. (PMID:24816778) identified as diagnostic of rare-earth-element (lanthanide)-coordinating XoxF-type dehydrogenases. Because the physiological metal cofactor of VPARA_00790 (Ca(2+) versus Ln(3+)) has not yet been measured experimentally, generalizing GO:0005509 to GO:0046872 (metal ion binding) avoids asserting unverified calcium specificity.
Proposed replacements: metal ion binding
Supporting Evidence:
PMID:24816778
While structures of MxaFI- and XoxF-MDH are conserved, also regarding the binding of PQQ, the accommodation of a REE requires the presence of a specific aspartate residue near the catalytic site.
GO:0016020 membrane
IEA
GO_REF:0000002 		REMOVE
Reason: False-positive InterPro2GO mapping on IPR017512 (matching the removal of GO:0016020 in METEA/xoxF1). VPARA_00790 (A0A0H2MDH4) has a cleavable N-terminal Sec signal peptide (residues 1-28) and zero transmembrane helices, and functions as a soluble periplasmic quinoprotein dehydrogenase in the periplasmic space (GO:0042597).
Supporting Evidence:
UniProtKB:A0A0H2MDH4
FT SIGNAL 1..28 FT /evidence="ECO:0000256|SAM:SignalP" FT CHAIN 29..608 FT /evidence="ECO:0000256|SAM:SignalP"
GO:0016491 oxidoreductase activity
IEA
GO_REF:0000117 		TOO GENERAL
Reason: True but uninformative parent term already subsumed by the accepted specific child annotation GO:0052933 (alcohol dehydrogenase (cytochrome c(L)) activity) on this entry.
Supporting Evidence:
UniProtKB:A0A0H2MDH4
DR NCBIfam; TIGR03075; PQQ_enz_alc_DH; 1.
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
IEA
GO_REF:0000002 		TOO GENERAL
Reason: True but broader parent term already subsumed by the accepted specific child annotation GO:0052933 (alcohol dehydrogenase (cytochrome c(L)) activity) on this entry.
Supporting Evidence:
UniProtKB:A0A0H2MDH4
DR NCBIfam; TIGR03075; PQQ_enz_alc_DH; 1.
GO:0052933 alcohol dehydrogenase (cytochrome c(L)) activity
IEA
GO_REF:0000003 		ACCEPT
Reason: VPARA_00790 (A0A0H2MDH4) is a periplasmic PQQ-dependent methanol/alcohol dehydrogenase (EC 1.1.2.7; NCBIfam TIGR03075, InterPro IPR017512, CDD cd10278) containing the conserved PQQ-binding (Glu83, Arg136, Thr180, Thr266) and proton-acceptor (Asp328) active-site architecture that oxidizes primary alcohols coupled to periplasmic cytochrome c reduction.
Supporting Evidence:
UniProtKB:A0A0H2MDH4
DR NCBIfam; TIGR03075; PQQ_enz_alc_DH; 1.
UniProtKB:A0A0H2MDH4
FT ACT_SITE 328 FT /note="Proton acceptor" FT /evidence="ECO:0000256|PIRSR:PIRSR617512-1"
GO:0070968 pyrroloquinoline quinone binding
IC
UniProtKB:A0A0H2MDH4 		NEW
Reason: Inferred by curator (IC) from the conserved PQQ-binding pocket (Glu83, Arg136, Thr180, and Thr266) and cofactor annotation in UniProtKB:A0A0H2MDH4.
Supporting Evidence:
UniProtKB:A0A0H2MDH4
CC -!- COFACTOR: CC Name=pyrroloquinoline quinone; Xref=ChEBI:CHEBI:58442; CC Evidence={ECO:0000256|PIRSR:PIRSR617512-2}; CC Note=Binds 1 PQQ group per subunit. {ECO:0000256|PIRSR:PIRSR617512-2};
GO:0006066 alcohol metabolic process
IC
UniProtKB:A0A0H2MDH4 		NEW
Reason: Inferred by curator (IC) from its core catalytic function as a periplasmic PQQ-dependent alcohol/methanol dehydrogenase (GO:0052933, NCBIfam TIGR03075, InterPro IPR017512).
Supporting Evidence:
UniProtKB:A0A0H2MDH4
DR NCBIfam; TIGR03075; PQQ_enz_alc_DH; 1.
GO:0042597 periplasmic space
IC
UniProtKB:A0A0H2MDH4 		NEW
Reason: Inferred by curator (IC) because VPARA_00790 (A0A0H2MDH4) possesses a cleavable N-terminal Sec signal peptide (residues 1-28) and zero transmembrane helices, localizing the mature soluble PQQ dehydrogenase (residues 29-608) to the Gram-negative periplasmic space.
Supporting Evidence:
UniProtKB:A0A0H2MDH4
FT SIGNAL 1..28 FT /evidence="ECO:0000256|SAM:SignalP" FT CHAIN 29..608 FT /evidence="ECO:0000256|SAM:SignalP"

Core Functions

Periplasmic PQQ-dependent alcohol/methanol dehydrogenase (EC 1.1.2.7) that oxidizes primary alcohols in the periplasmic space using pyrroloquinoline quinone (PQQ) and a Lewis-acid metal cofactor and transfers electrons to a periplasmic cytochrome c acceptor.

Molecular Function:
alcohol dehydrogenase (cytochrome c(L)) activity
Directly Involved In:
alcohol metabolic process
Cellular Locations:
periplasmic space
Supporting Evidence:
  • UniProtKB:A0A0H2MDH4
    DR NCBIfam; TIGR03075; PQQ_enz_alc_DH; 1.
  • UniProtKB:A0A0H2MDH4
    CC -!- COFACTOR: CC Name=pyrroloquinoline quinone; Xref=ChEBI:CHEBI:58442; CC Evidence={ECO:0000256|PIRSR:PIRSR617512-2}; CC Note=Binds 1 PQQ group per subunit. {ECO:0000256|PIRSR:PIRSR617512-2};

Binds one pyrroloquinoline quinone (PQQ) redox cofactor per subunit at the active site via Glu83, Arg136, Thr180, and Thr266.

Molecular Function:
pyrroloquinoline quinone binding
Directly Involved In:
alcohol metabolic process
Cellular Locations:
periplasmic space
Supporting Evidence:
  • UniProtKB:A0A0H2MDH4
    CC -!- COFACTOR: CC Name=pyrroloquinoline quinone; Xref=ChEBI:CHEBI:58442; CC Evidence={ECO:0000256|PIRSR:PIRSR617512-2}; CC Note=Binds 1 PQQ group per subunit. {ECO:0000256|PIRSR:PIRSR617512-2};

Coordinates a catalytic Lewis-acid metal ion (Ca(2+) or a trivalent lanthanide ion) at the active site via Glu198, Asn286, and Asp328 (within the Asp328-Phe329-Asp330 motif).

Molecular Function:
metal ion binding
Directly Involved In:
alcohol metabolic process
Cellular Locations:
periplasmic space
Supporting Evidence:
  • UniProtKB:A0A0H2MDH4
    FT BINDING 198 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /evidence="ECO:0000256|PIRSR:PIRSR617512-3" FT BINDING 266 FT /ligand="pyrroloquinoline quinone" FT /ligand_id="ChEBI:CHEBI:58442" FT /evidence="ECO:0000256|PIRSR:PIRSR617512-2" FT BINDING 286 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /evidence="ECO:0000256|PIRSR:PIRSR617512-3" FT BINDING 328 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /evidence="ECO:0000256|PIRSR:PIRSR617512-3"
  • PMID:24816778
    While structures of MxaFI- and XoxF-MDH are conserved, also regarding the binding of PQQ, the accommodation of a REE requires the presence of a specific aspartate residue near the catalytic site.

References

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Suggested Questions for Experts

Q: Does Variovorax paradoxus VPARA_00790 (A0A0H2MDH4), which possesses the XoxF-like Asp328-Phe329-Asp330 active-site motif, require trivalent lanthanide ions (La(3+), Ce(3+), Nd(3+)) or Ca(2+) for catalytic activity, and what is its physiological alcohol substrate spectrum in the rhizosphere?

Suggested Experiments

Experiment: Express and purify Variovorax paradoxus VPARA_00790 (A0A0H2MDH4) from cells grown with Ca(2+) versus light lanthanides (La(3+), Ce(3+), Pr(3+), Nd(3+)), determine bound metal stoichiometry by ICP-MS, and measure PQQ-dependent dehydrogenase kinetics across methanol, ethanol, and short-chain diols.

Hypothesis: Because VPARA_00790 contains the diagnostic Asp330 residue two positions C-terminal to the catalytic base Asp328 (328-DFD-330), it preferentially coordinates trivalent lanthanides over Ca(2+) to catalyze periplasmic alcohol oxidation.

Type: ICP-MS metal analysis and steady-state quinoprotein dehydrogenase kinetics

📚 Additional Documentation

Notes

(VPARA_00790-notes.md)

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