Curation Notes for Variovorax paradoxus S110 `pqqA` (`C5CPT7`, `PQQA_VARPS`, `Vapar_3057`)

Overview

UniProt Accession: C5CPT7 (PQQA_VARPS, reviewed Swiss-Prot)
Ordered Locus Name: Vapar_3057
Gene Symbol: pqqA
Organism: Variovorax paradoxus S110 (NCBITaxon:543728; [PMID:21183664 Complete genome sequence of the metabolically versatile plant growth-promoting endophyte Variovorax paradoxus S110., "The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes."])
Protein Function: 24-amino-acid ribosomally synthesized precursor peptide (MKWETPTATDLRFGFEITMYVSAR, HAMAP-Rule:MF_00656, InterPro:IPR011725, NCBIfam:TIGR02107) that provides the conserved Glu16 and Tyr20 residues (FT CROSSLNK 16..20) from which the redox cofactor pyrroloquinoline quinone (PQQ) is constructed (UniProtKB:C5CPT7).

PQQ is a ribosomally synthesized and post-translationally modified peptide (RiPP) cofactor ([PMID:25817994 PqqD is a novel peptide chaperone that forms a ternary complex with the radical S-adenosylmethionine protein PqqE in the pyrroloquinoline quinone biosynthetic pathway., "Pyrroloquinoline quinone (PQQ) is a product of a ribosomally synthesized and post-translationally modified pathway consisting of five conserved genes, pqqA-E."]).
PqqA is not a catalytic enzyme; instead, it is the polypeptide substrate whose N-terminal leader region is bound with nanomolar affinity by the peptide chaperone PqqD (Kd ~ 200 nM), positioning the conserved core motif E-I-T-M-Y (Glu16 and Tyr20 in C5CPT7) in the active site of the radical SAM enzyme PqqE ([PMID:32731194 Biogenesis of the peptide-derived redox cofactor pyrroloquinoline quinone., "The pqqA is translated into a short peptide that contains the fully conserved residues, glutamate and tyrosine; site-direct mutagenesis identified these two residues on PqqA as the best candidate for the precursor to PQQ (Figure 2A).[31]"]).
Pathway context is modeled in MODULE:pqq_biosynthesis.

GO:0018189 (pyrroloquinoline quinone biosynthetic process, IEA via UniProtKB-UniRule:UR000098299) -> ACCEPT (core biological process; PqqA is the obligate precursor peptide of PQQ biogenesis).

GO:0005829 (cytosol, IC, located_in) — PqqA is translated on cytosolic ribosomes as a 24-aa leaderless peptide and modified intracellularly by cytosolic PqqD/PqqE.