Modomics - A Database of RNA Modifications

ID Card:

Full name: rRNA guanine N-1-methyltransferase
Synonym: avilamycin resistance 23S rRNA methyltransferase
GI: 28380397
Orf: aviRa
COG: COG1041
UniProt: Q9F5K5
Structures: | 1O9G | 1O9H |
Alpha Fold Predicted Structure: AF-Q9F5K5-F1
Enzyme type: methyltransferase
Position of modification - modification: l:2535(2535) - m1G


PDB Structures:


1O9G

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The emergence of antibiotic-resistant bacterial strains is a widespread problem in contemporary medical practice and drug design. It is therefore important to elucidate the underlying mechanism in each case. The methyltransferase AviRa from Streptomyces viridochromogenes mediates resistance to the antibiotic avilamycin, which is closely related to evernimicin, an oligosaccharide antibiotic that has been used in medical studies. The structure of AviRa was determined by X-ray diffraction at 1.5A resolution. Phases were obtained from one selenomethionine residue introduced by site-directed mutagenesis. The chain-fold is similar to that of most methyltransferases, although AviRa contains two additional helices as a specific feature. A putative-binding site for the cofactor S-adenosyl-L-methionine was derived from homologous structures. It agrees with the conserved pattern of interacting amino acid residues. AviRa methylates a specific guanine base within the peptidyltransferase loop of the 23S ribosomal RNA. Guided by the target, the enzyme was docked to the cognate ribosomal surface, where it fit well into a deep cleft without contacting any ribosomal protein. The two additional alpha-helices of AviRa filled a depression in the surface. Since the transferred methyl group of the cofactor is in a pocket beneath the enzyme surface, the targeted guanine base has to flip out for methylation.

Download RCSB-PDB Structures:

Pdb Files   1O9G.pdb   1O9H.pdb  
Pdbx/mmCIF Files   1O9G.cif   1O9H.cif  


Protein sequence:

MSAYRHAVERIDSSDLACGVVLHSAPGYPAFPVRLATEIFQRALARLPGDGPVTLWDPCCGSGYLLTVLGLLHRRSLRQVIASDVDPAPLELAAKNLALLSPAGLTARELERREQSERFGKPSYLEAAQAARRLRERLTAEGGALPCAIRTADVFDPRALSAVLAGSAPDVVLTDLPYGERTHWEGQVPAQPVAGLLRSLASALPAHAVIAVTDRSRKIPVAPVKALERLKIGTRSAVLVRAADVLEAGP

Comments:

Methylation site was determined for E. coli rRNA.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m1G rRNA LSU 2535 LSU-23S prokaryotic cytosol 12828631   

Alpha Fold Predicted Structure:






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Protein sequence:

M S A Y R H A V E R I D S S D L A C G V V L H S A P G Y P A F P V R L A T E I F Q R A L A R L P G D G P V T L W D P C C G S G Y L L T V L G L L H R R S L R Q V I A S D V D P A P L E L A A K N L A L L S P A G L T A R E L E R R E Q S E R F G K P S Y L E A A Q A A R R L R E R L T A E G G A L P C A I R T A D V F D P R A L S A V L A G S A P D V V L T D L P Y G E R T H W E G Q V P A Q P V A G L L R S L A S A L P A H A V I A V T D R S R K I P V A P V K A L E R L K I G T R S A V L V R A A D V L E A G P

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q9F5K5-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9F5K5-F1.cif  
DSSP Secondary Structures   Q9F5K5.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The avilamycin resistance determinants AviRa and AviRb methylate 23S rRNA at the guanosine 2535 base and the uridine 2479 ribose. Treede I, Jakobsen L, Kirpekar F, Vester B, Weitnauer G, Bechthold A, Douthwaite S Mol Microbiol [details] 12828631 -
Crystal structure of the avilamycin resistance-conferring methyltransferase AviRa from Streptomyces viridochromogenes. Mosbacher TG, Bechthold A, Schulz GE J Mol Biol [details] 12742024 -
An ATP-binding cassette transporter and two rRNA methyltransferases are involved in resistance to avilamycin in the producer organism Streptomyces viridochromogenes Tu57. Weitnauer G, Gaisser S, Trefzer A, Stockert S, Westrich L, Quiros LM, Mendez C, Salas JA, Bechthold A Antimicrob Agents Chemother [details] 11181344 -