Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanine-N(7)-)-methyltransferase subunit TRM82
GI: 32363272
Orf: YDR165W
COG: COG2319
UniProt: Q03774
Structures: | 2VDU |
Alpha Fold Predicted Structure: AF-Q03774-F1
Complex: Trm8/Trm82


PDB Structures:


2VDU

Structure Description:

Title:
Classification:
Technique:

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  
Pdbx/mmCIF Files   2VDU.cif  


Protein sequence:

MSVIHPLQNLLTSRDGSLVFAIIKNCILSFKYQSPNHWEFAGKWSDDFDKIQESRNTTAKEQQGQSSENENENKKLKSNKGDSIKRTAAKVPSPGLGAPPIYSYIRNLRLTSDESRLIACADSDKSLLVFDVDKTSKNVLKLRKRFCFSKRPNAISIAEDDTTVIIADKFGDVYSIDINSIPEEKFTQEPILGHVSMLTDVHLIKDSDGHQFIITSDRDEHIKISHYPQCFIVDKWLFGHKHFVSSICCGKDYLLLSAGGDDKIFAWDWKTGKNLSTFDYNSLIKPYLNDQHLAPPRFQNENNDIIEFAVSKIIKSKNLPFVAFFVEATKCIIILEMSEKQKGDLALKQIITFPYNVISLSAHNDEFQVTLDNKESSGVQKNFAKFIEYNLNENSFVVNNEKSNEFDSAIIQSVQGDSNLVTKKEEIYPLYNVSSLRKHGEHYS

Comments:

It works in complex with Trm8 ( Matsumoto et al. 2007). 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). In the complex, it is required to stabilize and induce conformational changes of the catalytic subunit ( Leulliot et al. 2008).





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q03774-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q03774-F1.cif  
DSSP Secondary Structures   Q03774.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m(6)A methyltransferase. Bujnicki JM, Feder M, Radlinska M, Blumenthal RM J Mol Evol [details] 12355263 -
Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. Alexandrov A, Martzen MR, Phizicky EM RNA [details] 12403464 -
Structure of the yeast tRNA m7G methylation complex. Leulliot N, Chaillet M, Durand D, Ulryck N, Blondeau K, van Tilbeurgh H Structure [details] 18184583 -