Functional dichotomy in the 16S rRNA (m(1)A1408) methyltransferase family and control of catalytic activity via a novel tryptophan mediated loop reorganization

• Type of Material: Article
• Authors: Marta A. Witek, Emory University; Graeme Conn, Emory University
• Language: English
• Date: 2016-01-08
• Publisher: Oxford University Press (OUP): Policy C - Option B
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1093/nar/gkv1306
• Title of Journal or Parent Work: Nucleic Acids Research
• ISSN: 0305-1048
• Volume: 44
• Issue: 1
• Start Page: 342
• End Page: 353
• Grant/Funding Information: Funding for open access charge: National Institutes of Health-National Institute of Allergy and Infectious Diseases [R01-AI088025].; Use of the Advanced Photon Source, an Office of Science User Facility operated for the US Department of Energy (DOE) Office of Science by Argonne National Laboratory, was supported by the USA DOE [DE-AC02-06CH11357].; National Institutes of Health-National Institute of Allergy and Infectious Diseases [R01-AI088025 to G.L.C.]; The Auto-iTC200 instrument was purchased with support from the NSF MRI program [104177]; Winship Cancer Institute's shared resource program and the Biochemistry Department of Emory University.
• Keywords: INHIBITION; TRANSLOCATION; ESCHERICHIA-COLI; AMINOGLYCOSIDE ANTIBIOTICS; Biochemistry & Molecular Biology; Science & Technology; NPMA; HIV-1 PROTEASE; CATION-PI INTERACTIONS; RESISTANCE; VALIDATION; SUBUNIT; Life Sciences & Biomedicine
• Research Categories: Chemistry, Biochemistry

Abstract

Methylation of the bacterial small ribosomal subunit (16S) rRNA on the N1 position of A1408 confers exceptionally high-level resistance to a broad spectrum of aminoglycoside antibiotics. Here, we present a detailed structural and functional analysis of the Catenulisporales acidiphilia 16S rRNA (m1A1408) methyltransferase ('CacKam'). The apo CacKam structure closely resembles other m1A1408 methyltransferases within its conserved SAM-binding fold but the region linking core β strands 6 and 7 (the β6/7 linker') has a unique, extended structure that partially occludes the putative 16S rRNA binding surface, and sequesters the conserved and functionally critical W203 outside of the CacKam active site. Substitution of conserved residues in the SAM binding pocket reveals a functional dichotomy in the 16S rRNA (m1A1408) methyltransferase family, with two apparently distinct molecular mechanisms coupling cosubstrate/ substrate binding to catalytic activity. Our results additionally suggest that CacKam exploits the W203-mediated remodeling of the β6/7 linker as a novel mechanism to control 30S substrate recognition and enzymatic turnover.