PqqE (PqqA peptide cyclase, VPARA_00920, A0A0H2MPV4; also annotated as moaA1) in Variovorax paradoxus is a 383-amino-acid radical S-adenosyl-L-methionine (SAM) SPASM-domain metalloenzyme (EC 1.21.98.4, RHEA:56836; HAMAP MF_00660, InterPro IPR011843, NCBIfam TIGR02109, PANTHER PTHR11228:SF7) encoded at the 3' end of the pqqBCDE (VPARA_00950-VPARA_00920) gene cluster. Using a radical SAM [4Fe-4S] cluster coordinated by Cys22, Cys26, and Cys29 in its N-terminal core domain (residues 8-223) together with auxiliary iron-sulfur clusters in its C-terminal SPASM domain, PqqE reductively cleaves SAM to generate a 5'-deoxyadenosyl radical and catalyzes the first committed step of pyrroloquinoline quinone (PQQ) biosynthesis: formation of an intramolecular carbon-carbon cross-link between the conserved glutamate and tyrosine side chains of the PqqA precursor peptide presented by the peptide chaperone PqqD.
Definition: Catalysis of the reaction: [PQQ precursor protein] + S-adenosyl-L-methionine = Glu-Tyr cross-linked-[PQQ precursor protein] + 5'-deoxyadenosine + L-methionine + H+ (EC 1.21.98.4, RHEA:56836).
Justification: GO:0009975 (cyclase activity) is overly general for the radical-SAM-dependent intramolecular glutamate-tyrosine carbon-carbon cross-linking of PqqA defined by IUBMB EC 1.21.98.4 and RHEA:56836 (matching the proposed term in PSEPK/pqqE).
Parent term: cyclase activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Reason: Following the RADICAL_SAM project rule for generic domain-derived rows (projects/RADICAL_SAM.md), GO:0003824 is true but too general and is refined to GO:0009975 (cyclase activity), which this entry already carries. Proposed replacements: cyclase activity Supporting Evidence: UniProtKB:A0A0H2MPV4 DR NCBIfam; TIGR02109; PQQ_syn_pqqE; 1. |
| GO:0005506 iron ion binding | IEA GO_REF:0000104 | MODIFY | Reason: Following the RADICAL_SAM project rule for generic domain-derived rows (projects/RADICAL_SAM.md), PqqE coordinates iron as [4Fe-4S] clusters rather than as a mononuclear iron ion, so GO:0005506 is replaced by GO:0051539 (4 iron, 4 sulfur cluster binding). Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: UniProtKB:A0A0H2MPV4 CC -!- COFACTOR: CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; |
| GO:0009975 cyclase activity | IEA GO_REF:0000104 | ACCEPT | Reason: GO:0009975 (cyclase activity) is the most specific available Molecular Function term in GO for PqqE's radical SAM intramolecular Glu-Tyr peptide cross-linking reaction (EC 1.21.98.4, RHEA:56836; PMID:26961875), alongside a proposed_new_terms entry for PqqA peptide cyclase activity. Supporting Evidence: UniProtKB:A0A0H2MPV4 CC -!- FUNCTION: Catalyzes the cross-linking of a glutamate residue and a CC tyrosine residue in the PqqA protein as part of the biosynthesis of CC pyrroloquinoline quinone (PQQ). {ECO:0000256|HAMAP-Rule:MF_00660}. PMID:26961875 These results indicate that PqqE, in conjunction with PqqD, carries out the first step in PQQ biosynthesis: a radical-mediated formation of a new carbon-carbon bond between two amino acid side chains on PqqA. |
| GO:0018189 pyrroloquinoline quinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Reason: PqqE (VPARA_00920, A0A0H2MPV4) catalyzes the initiating committed step of pyrroloquinoline quinone biosynthesis by cross-linking the conserved glutamate and tyrosine residues of PqqA (PMID:26961875, PMID:32731194). Supporting Evidence: UniProtKB:A0A0H2MPV4 CC -!- PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. CC {ECO:0000256|HAMAP-Rule:MF_00660}. PMID:26961875 These results indicate that PqqE, in conjunction with PqqD, carries out the first step in PQQ biosynthesis: a radical-mediated formation of a new carbon-carbon bond between two amino acid side chains on PqqA. |
| GO:0046872 metal ion binding | IEA GO_REF:0000104 | MODIFY | Reason: Following the RADICAL_SAM project rule for generic domain-derived rows (projects/RADICAL_SAM.md), metal ion binding is replaced by GO:0051539 (4 iron, 4 sulfur cluster binding), which captures the actual metallocluster cofactor of PqqE. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: UniProtKB:A0A0H2MPV4 CC -!- COFACTOR: CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Reason: Following the RADICAL_SAM project rule for generic domain-derived rows (projects/RADICAL_SAM.md), GO:0051536 is correct but less specific than GO:0051539 (4 iron, 4 sulfur cluster binding), which is already present on this record. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: UniProtKB:A0A0H2MPV4 CC -!- COFACTOR: CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000120 | ACCEPT | Reason: PqqE binds a catalytic [4Fe-4S] cluster via Cys22, Cys26, and Cys29 in its N-terminal radical SAM domain (plus auxiliary Fe-S clusters in its C-terminal SPASM domain) to catalyze reductive cleavage of SAM (PMID:19746930, PMID:32731194, UniProtKB:A0A0H2MPV4). Supporting Evidence: UniProtKB:A0A0H2MPV4 CC -!- COFACTOR: CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; CC Evidence={ECO:0000256|HAMAP-Rule:MF_00660}; CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 CC cysteines and an exchangeable S-adenosyl-L-methionine. PMID:32731194 In the presence of reducing reagent and SAM, the [4Fe-4S] cluster in PqqE promotes the cleavage of SAM to 5’-deoxyadenosyl radical to initiate a series of steps culminating in a Glu-Tyr crosslink within PqqA. |
| GO:1904047 S-adenosyl-L-methionine binding | IEA GO_REF:0000104 | ACCEPT | Reason: PqqE binds S-adenosyl-L-methionine at the unique iron of its radical SAM [4Fe-4S] cluster and reductively cleaves it to generate the 5'-deoxyadenosyl radical that initiates PqqA Glu-Tyr cross-linking (PMID:19746930, PMID:26961875, UniProtKB:A0A0H2MPV4). Supporting Evidence: UniProtKB:A0A0H2MPV4 CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 CC cysteines and an exchangeable S-adenosyl-L-methionine. PMID:19746930 PqqE isolated anaerobically yields an active enzyme capable of cleaving SAM to methionine and 5'-deoxyadenosine in an uncoupled reaction |
| GO:0005829 cytosol | IC UniProtKB:A0A0H2MPV4 | NEW | Reason: Inferred by curator (IC) because V. paradoxus PqqE (A0A0H2MPV4) is a soluble 383-residue cytoplasmic radical SAM enzyme lacking signal peptides or transmembrane helices that forms a cytosolic PqqA-PqqD-PqqE ternary complex. Supporting Evidence: UniProtKB:A0A0H2MPV4 FT DOMAIN 8..223 FT /note="Radical SAM core" FT /evidence="ECO:0000259|PROSITE:PS51918" |
Loading supporting content…
Download this section (compressed HTML)Q: Which endogenous flavodoxin and flavodoxin reductase in Variovorax paradoxus supply the low-potential electrons required for coupled SAM cleavage and PqqA cross-linking by PqqE (VPARA_00920), and what cluster type ([2Fe-2S] vs [4Fe-4S]) occupies the SPASM AuxI site in vivo?
Experiment: Purify anaerobically reconstituted Variovorax paradoxus PqqE (A0A0H2MPV4) and assay SAM cleavage and Glu-Tyr cross-linking of synthetic PqqA in the presence of V. paradoxus PqqD (A0A0H2M992) by EPR spectroscopy and LC-HRMS/MS.
Hypothesis: Anaerobically reconstituted V. paradoxus PqqE catalyzes PqqD-dependent formation of the Glu-Tyr C-C cross-link in PqqA concurrent with 5'-deoxyadenosine and L-methionine generation.
Type: Anaerobic radical-SAM reconstitution, EPR spectroscopy, and LC-HRMS/MS
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)