Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (cytidine(56)-2'-O)-methyltransferase
Synonym: PH0461
GI: 14590372
COG: COG1303
UniProt: O58214
Structures: | 2YY8 |
Alpha Fold Predicted Structure: AF-O58214-F1
Enzyme type: methyltransferase
Position of modification - modification: t:56 - Um


PDB Structures:


2YY8

Structure Description:

Title: Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 2.48
R value free: 0.268
R value observed: 0.216
R value work: 0.216

Abstract of the PDB Structure's related Publication:

The conserved cytidine residue at position 56 of tRNA contributes to the maintenance of the L-shaped tertiary structure. aTrm56 catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Based on the amino acid sequence, aTrm56 is the most distant member of the SpoU family. Here, we determined the crystal structure of Pyrococcus horikoshii aTrm56 complexed with S-adenosyl-L-methionine at 2.48 A resolution. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot, and a unique C-terminal beta-hairpin. aTrm56 forms a dimer. The S-adenosyl-L-methionine binding and dimerization of aTrm56 were similar to those of the other SpoU members. A structure-based sequence alignment revealed that aTrm56 conserves only motif II, among the four signature motifs. However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate.

Download RCSB-PDB Structures:

Pdb Files   2YY8.pdb  
Pdbx/mmCIF Files   2YY8.cif  


Protein sequence:

MIKMIVVLRLGHRPERDKRVTTHVALTARAFGADGIIIASEEDEKVKESVEDVVKRWGGPFFIEFNRNWRKVMKEFTGVKVHLTMYGLHVDDVIEELKEKLKKGEDFMIIVGAEKVPREVYELADYNVAIGNQPHSEVAALAVLLDRLLEGKGLKKEFKGAKIKIVPQARGKKVVEVQGYAEQDKAEGKATPGKNWENSGFTGDNP

Comments:

The activity was tested in vitro on tRNAVal transcript.





Alpha Fold Predicted Structure:




Parsing response... [192064/192064]


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Protein sequence:

M I K M I V V L R L G H R P E R D K R V T T H V A L T A R A F G A D G I I I A S E E D E K V K E S V E D V V K R W G G P F F I E F N R N W R K V M K E F T G V K V H L T M Y G L H V D D V I E E L K E K L K K G E D F M I I V G A E K V P R E V Y E L A D Y N V A I G N Q P H S E V A A L A V L L D R L L E G K G L K K E F K G A K I K I V P Q A R G K K V V E V Q G Y A E Q D K A E G K A T P G K N W E N S G F T G D N P
20406080100120140160180200MIKMIVVLRLGHRPERDKRVTTHVALTARAFGADGIIIASEEDEKVKESVEDVVKRWGGPFFIEFNRNWRKVMKEFTGVKVHLTMYGLHVDDVIEELKEKLKKGEDFMIIVGAEKVPREVYELADYNVAIGNQPHSEVAALAVLLDRLLEGKGLKKEFKGAKIKIVPQARGKKVVEVQGYAEQDKAEGKATPGKNWENSGFTGDNPSequenceGHTSN

Enter the variants

Position

Original

Variant

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-O58214-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O58214-F1.cif  
DSSP Secondary Structures   O58214.dssp  





Publications:

Links:

_PubMed_