Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (cytidine(32)/guanosine(34)-2′-O)-methyltransferase
Synonym: Ybr1, FtsJ
GI: 586500
Orf: YBR061C
COG: COG0293
UniProt: P38238
Structures: | 6JP6 | 6JPL |
Alpha Fold Predicted Structure: AF-P38238-F1
Enzyme type: methyltransferase
Position of modification - modification: t:32 - Cm
t:34 - Gm
t:34 - ncm5Um


PDB Structures:


6JP6

Structure Description:

Title: The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 2.70
R value free: 0.239
R value observed: 0.196
R value work: 0.194

Abstract of the PDB Structure's related Publication:

The complex between Trm7 and Trm734 (Trm7-Trm734) from Saccharomyces cerevisiae catalyzes 2'-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7-Trm734 complex. Purified recombinant Trm7-Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7-Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7-Trm734. Small angle X-ray scattering reveals that Trm7-Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 β-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7-Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.

Download RCSB-PDB Structures:

Pdb Files   6JP6.pdb   6JPL.pdb  
Pdbx/mmCIF Files   6JP6.cif   6JPL.cif  


Protein sequence:

MGKSSKDKRDLYYRKAKEQGYRARSAFKLLQLNDQFHFLDDPNLKRVVDLCAAPGSWSQVLSRKLFDESPSSDKEDRKIVSVDLQPMSPIPHVTTLQADITHPKTLARILKLFGNEKADFVCSDGAPDVTGLHDLDEYVQQQLIMSALQLTACILKKGGTFVAKIFRGRDIDMLYSQLGYLFDKIVCAKPRSSRGTSLEAFIVCLGYNPPSNWTPKLDVNTSVDEFFQGCFLNKLCISDKLSHWNEEERNIAEFMACGSLQSFDSDATYHDLPSSVAGTSSSLDPVQSPTNPPYKKALELKRSGKLTRSV

Comments:

Carries out two succesive methylations of anticodon. Activity is stimulated by a not yet identified protein-cofactor (Lecointe, Grosjean, unpublished results).





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M G K S S K D K R D L Y Y R K A K E Q G Y R A R S A F K L L Q L N D Q F H F L D D P N L K R V V D L C A A P G S W S Q V L S R K L F D E S P S S D K E D R K I V S V D L Q P M S P I P H V T T L Q A D I T H P K T L A R I L K L F G N E K A D F V C S D G A P D V T G L H D L D E Y V Q Q Q L I M S A L Q L T A C I L K K G G T F V A K I F R G R D I D M L Y S Q L G Y L F D K I V C A K P R S S R G T S L E A F I V C L G Y N P P S N W T P K L D V N T S V D E F F Q G C F L N K L C I S D K L S H W N E E E R N I A E F M A C G S L Q S F D S D A T Y H D L P S S V A G T S S S L D P V Q S P T N P P Y K K A L E L K R S G K L T R S V
50100150200250300SequenceGHITBSN

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-P38238-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P38238-F1.cif  
DSSP Secondary Structures   P38238.dssp  





Publications:

Links:

_PubMed_