Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanine-N(7)-)-methyltransferase
GI: 32171782
Orf: YDL201W
COG: COG0220
UniProt: Q12009
Structures: | 2VDU | 2VDV |
Alpha Fold Predicted Structure: AF-Q12009-F1
Complex: Trm8/Trm82
Enzyme type: methyltransferase
Position of modification - modification: t:46 - m7G


PDB Structures:


2VDU

Structure Description:

Title: Structure of trm8-trm82, THE YEAST TRNA m7G methylation complex
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 2.4
R value free: 0.276
R value observed:
R value work: 0.228

Abstract of the PDB Structure's related Publication:

Loss of N7-methylguanosine (m7G) modification is involved in the recently discovered rapid tRNA degradation pathway. In yeast, this modification is catalyzed by the heterodimeric complex composed of a catalytic subunit Trm8 and a noncatalytic subunit Trm82. We have solved the crystal structure of Trm8 alone and in complex with Trm82. Trm8 undergoes subtle conformational changes upon Trm82 binding which explains the requirement of Trm82 for activity. Cocrystallization with the S-adenosyl-methionine methyl donor defines the putative catalytic site and a guanine binding pocket. Small-angle X-ray scattering in solution of the Trm8-Trm82 heterodimer in complex with tRNA(Phe) has enabled us to propose a low-resolution structure of the ternary complex which defines the tRNA binding mode of Trm8-Trm82 and the structural elements contributing to specificity.

Download RCSB-PDB Structures:

Pdb Files   2VDU.pdb   2VDV.pdb  
Pdbx/mmCIF Files   2VDU.cif   2VDV.cif  


Protein sequence:

MKAKPLSQDPGSKRYAYRINKEENRKELKHVKINESSLVQEGQKIDLPKKRYYRQRAHSNPFSDHQLEYPVSPQDMDWSKLYPYYKNAENGQMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNTASKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDPHFKQRKHKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAIL

Comments:

AdoMet is the methyl group donor. Heterodimer composed of two unrelated subunits: Trm8p (catalytic subunit) and Trm82p (cofactor, stimulates the activity of Trm8p, but is NOT absolutely essential). Works with Trm82p. Trm8p/Trm82p are not structuraly related. Belongs to the methyltransferase superfamily. TrmB family. This methyltransferase catalyzes the formation of N7-methylguanine at position 46 in tRNAs. This modification is required to maintain the stability of tRNAs, with its absence resulting in tRNA decay ( Alexandrov et al. 2006).





Alpha Fold Predicted Structure:




Parsing response... [275406/275406]


Clear Selection and Reset Camera

Protein sequence:

M K A K P L S Q D P G S K R Y A Y R I N K E E N R K E L K H V K I N E S S L V Q E G Q K I D L P K K R Y Y R Q R A H S N P F S D H Q L E Y P V S P Q D M D W S K L Y P Y Y K N A E N G Q M T K K V T I A D I G C G F G G L M I D L S P A F P E D L I L G M E I R V Q V T N Y V E D R I I A L R N N T A S K H G F Q N I N V L R G N A M K F L P N F F E K G Q L S K M F F C F P D P H F K Q R K H K A R I I T N T L L S E Y A Y V L K E G G V V Y T I T D V K D L H E W M V K H L E E H P L F E R L S K E W E E N D E C V K I M R N A T E E G K K V E R K K G D K F V A C F T R L P T P A I L
20406080100120140160180200220240260280SequenceGHTBSN

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-Q12009-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q12009-F1.cif  
DSSP Secondary Structures   Q12009.dssp  





Publications: