Nuclear Magnetic Resonance Structure and Binding Studies of PqqD, a Chaperone Required in the Biosynthesis of the Bacterial Dehydrogenase Cofactor Pyrroloquinoline Quinone

• Published in: Biochemistry (Easton) 2017-05, Vol.56 (21), p.2735-2746
• Main Authors: Latham, John A., Xia, Youlin, Klinman, Judith P., Wilmot, Carrie M.
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; biosynthesis; Methylobacterium extorquens; Methylobacterium extorquens - enzymology; Methylobacterium extorquens - metabolism; Models, Molecular; Molecular Chaperones - chemistry; Molecular Chaperones - metabolism; nuclear magnetic resonance spectroscopy; Nuclear Magnetic Resonance, Biomolecular; Oxidoreductases - chemistry; Oxidoreductases - metabolism; PQQ Cofactor - biosynthesis; PQQ Cofactor - chemistry; PQQ Cofactor - metabolism; Protein Conformation; scaffolding proteins
• ISSN: 0006-2960; 1520-4995; 1520-4995
• DOI: 10.1021/acs.biochem.7b00247

Biosynthesis of the ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is initiated when the precursor peptide, PqqA, is recognized and bound by the RiPP precursor peptide recognition element (RRE), PqqD, for presentation to the first enzyme in the pathway, PqqE. Unlike other RiPP-producing, postribosomal peptide synthesis (PRPS) pathways in which the RRE is a component domain of the first enzyme, PqqD is predominantly a separate scaffolding protein that forms a ternary complex with the precursor peptide and first tailoring enzyme. As PqqD is a stable, independent RRE, this makes the PQQ pathway an ideal PRPS model system for probing RRE interactions using nuclear magnetic resonance (NMR). Herein, we present both the solution NMR structure of Methylobacterium extorquens PqqD and results of 1H–15N HSQC binding experiments that identify the PqqD residues involved in binding the precursor peptide, PqqA, and the enzyme, PqqE. The reported structural model for an independent RRE, along with the mapped binding surfaces, will inform future efforts both to understand and to manipulate PRPS pathways.