title: Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure.
abstract: N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m(2)G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m(2)G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05A(.) The structure closely resembles RsmC rRNA methyltransferase, specific for m(2)G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m(2)G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed.
authors.affiliation: Department of Bioinformatics and Bioengineering, Moscow State University, Moscow 119992, Russia.
authors.forename: Dmitry V
authors.initials: DV
authors.lastname: Lesnyak
authors.forename: Jerzy
authors.initials: J
authors.lastname: Osipiuk
authors.forename: Tatiana
authors.initials: T
authors.lastname: Skarina
authors.forename: Petr V
authors.initials: PV
authors.lastname: Sergiev
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Bogdanov
authors.forename: Aled
authors.initials: A
authors.lastname: Edwards
authors.forename: Alexei
authors.initials: A
authors.lastname: Savchenko
authors.forename: Andrzej
authors.initials: A
authors.lastname: Joachimiak
authors.forename: Olga A
authors.initials: OA
authors.lastname: Dontsova
mesh_terms: D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D006147:Guanine; D008745:Methylation; D008780:Methyltransferases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding / Q000502:physiology; D017434:Protein Structure, Tertiary; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D006147:Guanine; D008780:Methyltransferases; C518826:RsmD protein, E coli