title: PqqD is a novel peptide chaperone that forms a ternary complex with the radical S-adenosylmethionine protein PqqE in the pyrroloquinoline quinone biosynthetic pathway.
abstract: Pyrroloquinoline quinone (PQQ) is a product of a ribosomally synthesized and post-translationally modified pathway consisting of five conserved genes, pqqA-E. PqqE is a radical S-adenosylmethionine (RS) protein with a C-terminal SPASM domain, and is proposed to catalyze the formation of a carbon-carbon bond between the glutamate and tyrosine side chains of the peptide substrate PqqA. PqqD is a 10-kDa protein with an unknown function, but is essential for PQQ production. Recently, in Klebsiella pneumoniae (Kp), PqqD and PqqE were shown to interact; however, the stoichiometry and KD were not obtained. Here, we show that the PqqE and PqqD interaction transcends species, also occurring in Methylobacterium extorquens AM1 (Me). The stoichiometry of the MePqqD and MePqqE interaction is 1:1 and the KD, determined by surface plasmon resonance spectroscopy (SPR), was found to be ∼12 μm. Moreover, using SPR and isothermal calorimetry techniques, we establish for the first time that MePqqD binds MePqqA tightly (KD ∼200 nm). The formation of a ternary MePqqA-D-E complex was captured by native mass spectrometry and the KD for the MePqqAD-MePqqE interaction was found to be ∼5 μm. Finally, using a bioinformatic analysis, we found that PqqD orthologues are associated with the RS-SPASM family of proteins (subtilosin, pyrroloquinoline quinone, anaerobic sulfatase maturating enzyme, and mycofactocin), all of which modify either peptides or proteins. In conclusion, we propose that PqqD is a novel peptide chaperone and that PqqD orthologues may play a similar role in peptide modification pathways that use an RS-SPASM protein.
authors.affiliation: From the Departments of Chemistry and Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720.
authors.forename: John A
authors.initials: JA
authors.lastname: Latham
authors.affiliation: From the Departments of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720.
authors.forename: Anthony T
authors.initials: AT
authors.lastname: Iavarone
authors.affiliation: From the Departments of Chemistry and Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720.
authors.forename: Ian
authors.initials: I
authors.lastname: Barr
authors.affiliation: From the Departments of Chemistry and Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720.
authors.forename: Prerak V
authors.initials: PV
authors.lastname: Juthani
authors.affiliation: From the Departments of Chemistry and Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720 klinman@berkeley.edu.
authors.forename: Judith P
authors.initials: JP
authors.lastname: Klinman
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010450:Endopeptidases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013058:Mass Spectrometry; D020601:Methylobacterium extorquens / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018832:Molecular Chaperones / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020349:Surface Plasmon Resonance
chemical_list: D001426:Bacterial Proteins; D018832:Molecular Chaperones; D046912:Multiprotein Complexes; C091163:PqqD protein, Methylobacterium extorquens; D010450:Endopeptidases; C098959:PqqE protein, Methylobacterium extorquens
keywords: PqqD; PqqE; peptide biosynthesis; peptide interaction; protein complex; quinone; small-angle x-ray scattering (SAXS)
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