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Title: Structural Rearrangements in the Active Site of the Thermus thermophilus 16S rRNA Methyltransferase KsgA in a Binary Complex with 5'-Methylthioadenosine

Abstract

Posttranscriptional modification of ribosomal RNA (rRNA) occurs in all kingdoms of life. The S-adenosyl-l-methionine-dependent methyltransferase KsgA introduces the most highly conserved rRNA modification, the dimethylation of A1518 and A1519 of 16S rRNA. Loss of this dimethylation confers resistance to the antibiotic kasugamycin. Here, we report biochemical studies and high-resolution crystal structures of KsgA from Thermus thermophilus. Methylation of 30S ribosomal subunits by T. thermophilus KsgA is more efficient at low concentrations of magnesium ions, suggesting that partially unfolded RNA is the preferred substrate. The overall structure is similar to that of other methyltransferases but contains an additional ?-helix in a novel N-terminal extension. Comparison of the apoenzyme with complex structures with 5?-methylthioadenosine or adenosine bound in the cofactor-binding site reveals novel features when compared with related enzymes. Several mobile loop regions that restrict access to the cofactor-binding site are observed. In addition, the orientation of residues in the substrate-binding site indicates that conformational changes are required for binding two adjacent residues of the substrate rRNA.

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States). National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
980530
Report Number(s):
BNL-93448-2010-JA
Journal ID: ISSN 0022-2836; JMOBAK; TRN: US201015%%1915
DOE Contract Number:  
DE-AC02-98CH10886
Resource Type:
Journal Article
Journal Name:
Journal of Molecular Biology
Additional Journal Information:
Journal Volume: 388; Journal ID: ISSN 0022-2836
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; ADENOSINE; ANTIBIOTICS; CONFORMATIONAL CHANGES; CRYSTAL STRUCTURE; ENZYMES; MAGNESIUM IONS; METHYLATION; MODIFICATIONS; ORIENTATION; RESIDUES; RIBOSOMAL RNA; RNA; SUBSTRATES; national synchrotron light source

Citation Formats

Demirci, H, Belardinelli, R, Seri, E, Gregory, S, Gualerzi, C, Dahlberg, A, and Jogl, G. Structural Rearrangements in the Active Site of the Thermus thermophilus 16S rRNA Methyltransferase KsgA in a Binary Complex with 5'-Methylthioadenosine. United States: N. p., 2009. Web. doi:10.1016/j.jmb.2009.02.066.
Demirci, H, Belardinelli, R, Seri, E, Gregory, S, Gualerzi, C, Dahlberg, A, & Jogl, G. Structural Rearrangements in the Active Site of the Thermus thermophilus 16S rRNA Methyltransferase KsgA in a Binary Complex with 5'-Methylthioadenosine. United States. https://doi.org/10.1016/j.jmb.2009.02.066
Demirci, H, Belardinelli, R, Seri, E, Gregory, S, Gualerzi, C, Dahlberg, A, and Jogl, G. 2009. "Structural Rearrangements in the Active Site of the Thermus thermophilus 16S rRNA Methyltransferase KsgA in a Binary Complex with 5'-Methylthioadenosine". United States. https://doi.org/10.1016/j.jmb.2009.02.066.
@article{osti_980530,
title = {Structural Rearrangements in the Active Site of the Thermus thermophilus 16S rRNA Methyltransferase KsgA in a Binary Complex with 5'-Methylthioadenosine},
author = {Demirci, H and Belardinelli, R and Seri, E and Gregory, S and Gualerzi, C and Dahlberg, A and Jogl, G},
abstractNote = {Posttranscriptional modification of ribosomal RNA (rRNA) occurs in all kingdoms of life. The S-adenosyl-l-methionine-dependent methyltransferase KsgA introduces the most highly conserved rRNA modification, the dimethylation of A1518 and A1519 of 16S rRNA. Loss of this dimethylation confers resistance to the antibiotic kasugamycin. Here, we report biochemical studies and high-resolution crystal structures of KsgA from Thermus thermophilus. Methylation of 30S ribosomal subunits by T. thermophilus KsgA is more efficient at low concentrations of magnesium ions, suggesting that partially unfolded RNA is the preferred substrate. The overall structure is similar to that of other methyltransferases but contains an additional ?-helix in a novel N-terminal extension. Comparison of the apoenzyme with complex structures with 5?-methylthioadenosine or adenosine bound in the cofactor-binding site reveals novel features when compared with related enzymes. Several mobile loop regions that restrict access to the cofactor-binding site are observed. In addition, the orientation of residues in the substrate-binding site indicates that conformational changes are required for binding two adjacent residues of the substrate rRNA.},
doi = {10.1016/j.jmb.2009.02.066},
url = {https://www.osti.gov/biblio/980530}, journal = {Journal of Molecular Biology},
issn = {0022-2836},
number = ,
volume = 388,
place = {United States},
year = {Thu Jan 01 00:00:00 EST 2009},
month = {Thu Jan 01 00:00:00 EST 2009}
}