Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA

Erica L Schwalm; Tyler L Grove; Squire J Booker; Amie K Boal

doi:10.1126/science.aad5367

Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA

Science. 2016 Apr 15;352(6283):309-12. doi: 10.1126/science.aad5367.

Authors

Erica L Schwalm¹, Tyler L Grove¹, Squire J Booker², Amie K Boal³

Affiliations

¹ Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
² Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA. Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA 16802, USA. squire@psu.edu akb20@psu.edu.
³ Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA. Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. squire@psu.edu akb20@psu.edu.

Abstract

RlmN is a dual-specificity RNA methylase that modifies C2 of adenosine 2503 (A2503) in 23S rRNA and C2 of adenosine 37 (A37) in several Escherichia coli transfer RNAs (tRNAs). A related methylase, Cfr, modifies C8 of A2503 via a similar mechanism, conferring resistance to multiple classes of antibiotics. Here, we report the x-ray structure of a key intermediate in the RlmN reaction, in which a Cys(118)→Ala variant of the protein is cross-linked to a tRNA(Glu)substrate through the terminal methylene carbon of a formerly methylcysteinyl residue and C2 of A37. RlmN contacts the entire length of tRNA(Glu), accessing A37 by using an induced-fit strategy that completely unfolds the tRNA anticodon stem-loop, which is likely critical for recognition of both tRNA and ribosomal RNA substrates.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Adenosine / chemistry
Alanine / chemistry
Alanine / genetics
Amino Acid Substitution
Anticodon / chemistry
Catalytic Domain
Crystallography, X-Ray
Cysteine / chemistry
Cysteine / genetics
Escherichia coli Proteins / chemistry*
Escherichia coli Proteins / genetics
Escherichia coli Proteins / ultrastructure*
Methylation
Methyltransferases / chemistry*
Methyltransferases / genetics
Methyltransferases / ultrastructure*
Nucleic Acid Conformation
Protein Structure, Tertiary
RNA, Bacterial / chemistry*
RNA, Transfer, Glu / chemistry*
RNA, Transfer, Glu / ultrastructure*
S-Adenosylmethionine / chemistry

Substances

Anticodon
Escherichia coli Proteins
RNA, Bacterial
RNA, Transfer, Glu
S-Adenosylmethionine
Methyltransferases
RlmN protein, E coli
Adenosine
Cysteine
Alanine

Associated data

PDB/5HR6
PDB/5HR7

Abstract

Publication types

MeSH terms

Substances

Associated data

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