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: rRNA methyltransferase aviRa from Streptomyces viridochromogenes at 1.5A
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 1.5
R value free: 0.202
R value observed: 0.17
R value work: 0.169

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.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

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
20406080100120140160180200220240SequenceGHTBSN

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: