Crystal Structure and Function of PqqF Protein in the Pyrroloquinoline Quinone Biosynthetic Pathway

Abstract

Pyrroloquinoline quinone (PQQ) has received considerable attention due to its numerous important physiological functions. PqqA is a precursor peptide of PQQ with two conserved residues: glutamate and tyrosine. After linkage of the C␥ of glutamate and C⑀ of tyrosine by PqqE, these two residues are hypothesized to be cleaved from PqqA by PqqF. The linked glutamate and tyrosine residues are then used to synthesize PQQ. Here, we demonstrated that the pqqF gene is essential for PQQ biosynthesis as deletion of it eliminated the inhibition of prodigiosin production by glucose. We further determined the crystal structure of PqqF, which has a closed clamshell-like shape. The PqqF consists of two halves composed of an N-and a C-terminal lobe. The PqqF-N and PqqF-C lobes form a chamber with the volume of the cavity of ϳ9400 Å 3 . The PqqF structure conforms to the general structure of inverzincins. Compared with the most thoroughly characterized inverzincin insulin-degrading enzyme, the size of PqqF chamber is markedly smaller, which may define the specificity for its substrate PqqA. Furthermore, the 14-amino acid-residue-long tag formed by the N-terminal tag from expression vector precisely protrudes into the counterpart active site; this N-terminal tag occupies the active site and stabilizes the closed, inactive conformation. His-48, His-52, Glu-129 and His-14 from the N-terminal tag coordinate with the zinc ion. Glu-51 acts as a base catalyst. The observed histidine residue-mediated inhibition may be applicable for the design of a peptide for the inhibition of M16 metalloproteases.Pyrroloquinoline quinone (PQQ), 4 an aromatic orthoquinone, has been recognized as the third class of redox cofactors in addition to the well known cofactors, nicotinamide (NAD(P) ϩ ) and flavin (FAD, FMN) (1). PQQ was first identified from methanol dehydrogenase in methylotrophic bacteria (2), and several bacterial dehydrogenases, such as glucose dehydrogenases, quinate dehydrogenase, and alcohol dehydrogenase, were later found to be quinoproteins (3-5). Recently, sugar oxidoreductase in the basidiomycete Coprinopsis cinerea (6), 2-keto-D-glucose dehydrogenase from Pseudomonas aureofaciens (7) and pyranose dehydrogenase from C. cinerea (8) were all characterized as novel PQQ-dependent enzymes. Free PQQ has been identified in a wide variety of foods (9) and milk (10). PQQ is an essential nutrient for proper growth and development in mice (11). The strong-antioxidant capacity of PQQ protects living cells and biomolecules from oxidative stress in vivo and in vitro (12, 13). Furthermore, PQQ exerts a protective effect against ultraviolet irradiation-induced human dermal fibroblast senescence in vitro (14) and suppresses the serum low density cholesterol level to prevent various diseases (15). In addition, PQQ may improve skin conditions and slow the progression of osteoarthritis (16).The chemical structure of PQQ was determined in 1980 (17). Since then gene clusters involved in the synthesis of PQQ from different bacteria that range from 4 genes ...

Rhizosphere-Associated Pseudomonas Suppress Local Root Immune Responses by Gluconic Acid-Mediated Lowering of Environmental pH

“…PqqF is a putative protease required for pyrroloquinoline quinone (PQQ) biosynthesis [18]. PQQ is a redox active molecule, functioning as a cofactor for many bacterial dehydrogenases involved in the utilization of carbon sources [19].…”

Effect of the additive of pyrroloquinoline quinone on waste glycerol bioconversion to dihydroxyacetone

“…Pyrroloquinoline quinone is soluble in water, aromatic orthoquinone from the third class of redox cofactors [Wei et al 2016, Ikemoto et al 2017. It is composed of glutamate and tyrosine, which are most probably provided by PqqA protein [Hölscher and Goörisch 2006].…”

“…The coenzyme PQQ synthesis protein PqqB is engaged in PQQ transport to the periplasmic space wherein dehydrogenases are accumulated [Metlitzky et al 2012]. The coenzyme PQQ synthesis protein PqqC catalyzes the last stage of PQQ synthesis [Magnusson et al 2004], whereas the coenzyme PQQ synthesis protein PqqD participates in coding a 29-amino acid peptide claimed to be a precursor of PQQ biosynthesis [Wei et al 2016].…”

A two-component protease in Methylorubrum extorquens with high activity toward the peptide precursor of the redox cofactor pyrroloquinoline quinone

“…FS14. Wei et al (29) crystallized this protein and assigned it as an M16A peptidase of the ME clan, characterized as containing the zinc-binding motif HXXEH (30). Earlier, the Lidstrom group (31) had identified two gene clusters required for the growth of Mex AM1 mutants on methanol named pqqDGCBA and pqqEF.…”