Substrate Recognition and Modification by a Pathogen-Associated Aminoglycoside Resistance 16S rRNA Methyltransferase

• Type of Material: Article
• Authors: Kellie Vinal, Emory University; Graeme L Conn, Emory University
• Language: English
• Date: 2017-05-01
• Publisher: American Society for Microbiology
• Publication Version: Final Published Version
• Copyright Statement: © 2017 American Society for Microbiology. All Rights Reserved.
• Final Published Version (URL): http://dx.doi.org/10.1128/AAC.00077-17
• Title of Journal or Parent Work: Antimicrobial Agents and Chemotherapy
• ISSN: 0066-4804
• Volume: 61
• Issue: 5
• Start Page: AAC.00077-17
• End Page: AAC.00077-17
• Grant/Funding Information: This work was supported by the National Institutes of Health-National Institute of Allergy and Infectious Diseases (R01-AI088025 to G.L.C.).
• Keywords: SUBUNIT; Life Sciences & Biomedicine; Science & Technology; METHYLATION; RNA binding proteins; SITE; Pharmacology & Pharmacy; methyltransferase; SPECIFICITY; STRUCTURAL BASIS; NPMA; rRNA modification; Microbiology; M(1)A1408 METHYLTRANSFERASE; INSIGHTS; PLASMID; antibiotic resistance; aminoglycosides; CRYSTAL-STRUCTURES; ribosomes
• Research Categories: Biology, Microbiology; Biology, Genetics; Chemistry, Biochemistry

Abstract

The pathogen-associated 16S rRNA methyltransferase NpmA catalyzes m1A1408 modification to block the action of structurally diverse aminoglycoside antibiotics. Here, we describe the development of a fluorescence polarization binding assay and its use, together with complementary functional assays, to dissect the mechanism of NpmA substrate recognition. These studies reveal that electrostatic interactions made by the NpmA β2/3 linker collectively are critical for docking of NpmA on a conserved 16S rRNA tertiary surface. In contrast, other NpmA regions (β5/β6 and β6/β7 linkers) contain several residues critical for optimal positioning of A1408 but are largely dispensable for 30S binding. Our data support a model for NpmA action in which 30S binding and adoption of a catalytically competent state are distinct: docking on 16S rRNA via the β2/3 linker necessarily precedes functionally critical 30S substrate-driven conformational changes elsewhere in NpmA. This model is also consistent with catalysis being completely positional in nature, as the most significant effects on activity arise from changes that impact binding or stabilization of the flipped A1408 conformation. Our results provide a molecular framework for aminoglycoside resistance methyltransferase action that may serve as a functional paradigm for related enzymes and a starting point for development of inhibitors of these resistance determinants.