3FUT

Apo-form of T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in space group P21212

Summary for 3FUT

• Entry DOI: 10.2210/pdb3fut/pdb
• Related: 3FUU 3FUV 3FUW 3FUX
• Descriptor: Dimethyladenosine transferase (2 entities in total)
• Functional Keywords: methyltransferase, dimethyltransferase, dual-specific methyltransferase, 16s rrna methyltransferase, translation, antibiotic resistance, rna-binding, rrna processing, s-adenosyl-l-methionine, transferase
• Biological source: Thermus thermophilus
• Cellular location: Cytoplasm : Q5SM60
• Total number of polymer chains: 2
• Total formula weight: 60005.47

Authors

Demirci, H.,Belardinelli, R.,Seri, E.,Gregory, S.T.,Gualerzi, C.,Dahlberg, A.E.,Jogl, G. (deposition date: 2009-01-14, release date: 2009-03-31, Last modification date: 2024-10-16)

Primary citation

Demirci, H.,Belardinelli, R.,Seri, E.,Gregory, S.T.,Gualerzi, C.,Dahlberg, A.E.,Jogl, G.
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.
J.Mol.Biol., 388:271-282, 2009

PubMed 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 alpha-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.

PubMed: 19285505
DOI: 10.1016/j.jmb.2009.02.066

Experimental method

X-RAY DIFFRACTION (1.52 Å)