Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanine(37)-N1)-methyltransferase Trm5b
Synonym: MJ0883
GI: 15669073
COG: COG2520
UniProt: Q58293
Structures: | 2ZZM | 2ZZN | 3AY0 | 2YX1 |
Alpha Fold Predicted Structure: AF-Q58293-F1
Enzyme type: methyltransferase
Position of modification - modification: t:37 - m1G


PDB Structures:


2ZZM

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Methylation of the N1 atom of guanosine at position 37 in tRNA, the position 3'-adjacent to the anticodon, generates the modified nucleoside m(1)G37. In archaea and eukaryotes, m(1)G37 synthesis is catalyzed by tRNA(m(1)G37)methyltransferase (archaeal or eukaryotic Trm5, a/eTrm5). Here we report the crystal structure of archaeal Trm5 (aTrm5) from Methanocaldococcus jannaschii (formerly known as Methanococcus jannaschii) in complex with the methyl donor analogue at 2.2 A resolution. The crystal structure revealed that the entire protein is composed of three structural domains, D1, D2, and D3. In the a/eTrm5 primary structures, D2 and D3 are highly conserved, while D1 is not conserved. The D3 structure is the Rossmann fold, which is the hallmark of the canonical class-I methyltransferases. The a/eTrm5-defining domain, D2, exhibits structural similarity to some class-I methyltransferases. In contrast, a DALI search with the D1 structure yielded no structural homologues. In the crystal structure, D3 contacts both D1 and D2. The residues involved in the D1:D3 interactions are not conserved, while those participating in the D2:D3 interactions are well conserved. D1 and D2 do not contact each other, and the linker between them is disordered. aTrm5 fragments corresponding to the D1 and D2-D3 regions were prepared in a soluble form. The NMR analysis of the D1 fragment revealed that D1 is well folded by itself, and it did not interact with either the D2-D3 fragment or the tRNA. The NMR analysis of the D2-D3 fragment revealed that it is well folded, independently of D1, and that it interacts with tRNA. Furthermore, the D2-D3 fragment was as active as the full-length enzyme for tRNA methylation. The positive charges on the surface of D2-D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2-D3 region plays the major role in tRNA methylation.

Download RCSB-PDB Structures:

Pdb Files   2YX1.pdb   2ZZM.pdb   2ZZN.pdb   3AY0.pdb  
Pdbx/mmCIF Files   2YX1.cif   2ZZM.cif   2ZZN.cif   3AY0.cif  


Protein sequence:

MPLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEKKIIKKPSFREIISKKYRKEIDEGLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRKSEVKGEFRVRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVKSYAPREYILALDFKINKK

Comments:




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m1G RNA tRNA 37 GCA GCA tRNACysGCA anticodon-loop Prokaryotic Cytosol 16768442   
G:m1G RNA tRNA 37 UAG UAG tRNALeuUAG anticodon-loop Prokaryotic Cytosol 19749755   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q58293-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q58293-F1.cif  
DSSP Secondary Structures   Q58293.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5. Christian T, Lahoud G, Liu C, Hoffmann K, Perona JJ, Hou YM RNA [details] 20980671 -
Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline. Christian T, Evilia C, Hou YM Biochemistry [details] 16768442 -
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Goto-Ito S, Ito T, Kuratani M, Bessho Y, Yokoyama S Nat Struct Mol Biol [details] 19749755 -
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Goto-Ito S, Ito T, Ishii R, Muto Y, Bessho Y, Yokoyama S Proteins [details] 18384044 -
Conservation of structure and mechanism by Trm5 enzymes. Christian T, Gamper H, Hou YM... RNA [details] 23887145 -

Links:

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