Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (adenine(22)-N(1))-methyltransferase
GI: 332278123
Orf: YqfN
UniProt: P54471
Structures: | 6Q56 |
Alpha Fold Predicted Structure: AF-P54471-F1
Enzyme type: methyltransferase
Position of modification - modification: t:22 - m1A


PDB Structures:


6Q56

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

1-Methyladenosine (m1A) is a modified nucleoside found at positions 9, 14, 22 and 58 of tRNAs, which arises from the transfer of a methyl group onto the N1-atom of adenosine. The yqfN gene of Bacillus subtilis encodes the methyltransferase TrmK (BsTrmK) responsible for the formation of m1A22 in tRNA. Here, we show that BsTrmK displays a broad substrate specificity, and methylates seven out of eight tRNA isoacceptor families of B. subtilis bearing an A22. In addition to a non-Watson-Crick base-pair between the target A22 and a purine at position 13, the formation of m1A22 by BsTrmK requires a full-length tRNA with intact tRNA elbow and anticodon stem. We solved the crystal structure of BsTrmK showing an N-terminal catalytic domain harbouring the typical Rossmann-like fold of Class-I methyltransferases and a C-terminal coiled-coil domain. We used NMR chemical shift mapping to drive the docking of BstRNASer to BsTrmK in complex with its methyl-donor cofactor S-adenosyl-L-methionine (SAM). In this model, validated by methyltransferase activity assays on BsTrmK mutants, both domains of BsTrmK participate in tRNA binding. BsTrmK recognises tRNA with very few structural changes in both partner, the non-Watson-Crick R13-A22 base-pair positioning the A22 N1-atom close to the SAM methyl group.

Download RCSB-PDB Structures:

Pdb Files   6Q56.pdb  
Pdbx/mmCIF Files   6Q56.cif  


Protein sequence:

MADIGSDHAYLPCYAVLNHKASGAIAGEITDGPFLSAKRQVEKSGLNSHISVRQGDGLEVIKKGEADAITIAGMGGALIAHILEAGKDKLTGKERLILQPNIHAVHIREWLYKERYALIDEVILEEDGKCYEVLVAEAGDRDAAYDGISLSAGMLVGPFLAKEKNAVFLKKWTQELQHTQSIYEQISQAADTEQNKQKLKELADRMELLKEVIDHG

Comments:




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:m1A RNA tRNA 22 GGA GGA D-loop Prokaryotic Cytosol

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P54471-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P54471-F1.cif  
DSSP Secondary Structures   P54471.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK). Roovers M, Kaminska KH, Tkaczuk KL, Gigot D, Droogmans L, Bujnicki JM Nucleic Acids Res [details] 18420655 -