Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanine-N(7)-)-methyltransferase
Synonym: ytmQ
GI: 14194920
COG: COG0220
UniProt: O34522
Structures: | 2FCA | 7NYB | 7NZI | 7NZJ |
Alpha Fold Predicted Structure: AF-O34522-F1
Enzyme type: methyltransferase
Position of modification - modification: t:46 - m7G


PDB Structures:


2FCA

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The structure of Bacillus subtilis TrmB (BsTrmB), the tRNA (m7G46) methyltransferase, was determined at a resolution of 2.1 A. This is the first structure of a member of the TrmB family to be determined by X-ray crystallography. It reveals a unique variant of the Rossmann-fold methyltransferase (RFM) structure, with the N-terminal helix folded on the opposite site of the catalytic domain. The architecture of the active site and a computational docking model of BsTrmB in complex with the methyl group donor S-adenosyl-L-methionine and the tRNA substrate provide an explanation for results from mutagenesis studies of an orthologous enzyme from Escherichia coli (EcTrmB). However, unlike EcTrmB, BsTrmB is shown here to be dimeric both in the crystal and in solution. The dimer interface has a hydrophobic core and buries a potassium ion and five water molecules. The evolutionary analysis of the putative interface residues in the TrmB family suggests that homodimerization may be a specific feature of TrmBs from Bacilli, which may represent an early stage of evolution to an obligatory dimer.

Download RCSB-PDB Structures:

Pdb Files   2FCA.pdb   7NYB.pdb   7NZI.pdb   7NZJ.pdb  
Pdbx/mmCIF Files   2FCA.cif   7NYB.cif   7NZI.cif   7NZJ.cif  


Protein sequence:

MRMRHKPWADDFLAENADIAISNPADYKGKWNTVFGNDNPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTAVQKVKDSEAQNVKLLNIDADTLTDVFEPGEVKRVYLNFSDPWPKKRHEKRRLTYSHFLKKYEEVMGKGGSIHFKTDNRGLFEYSLKSFSEYGLLLTYVSLDLHNSNLEGNIMTEYEEKFSALGQPIYRAEVEWRT

Comments:

AdoMet is the methyl group donor. The activity was tested in vitro on tRNAPhe transctipt.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m7G RNA tRNA 46 #AA #AA tRNAPhe#AA V-loop Prokaryotic Cytosol 16600901   

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-O34522-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O34522-F1.cif  
DSSP Secondary Structures   O34522.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase. Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L Nucleic Acids Res [details] 16600901 -

Links:

_PubMed_