Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA modification GTPase MnmE
Synonym: TrmE
GI: 15643037
COG: COG0486
UniProt: Q9WYA4
Structures: | 1XZP | 1XZQ |
Alpha Fold Predicted Structure: AF-Q9WYA4-F1
Complex: MnmE/MnmG
Enzyme type: GTPase
Position of modification - modification: t:34 - cmnm5s2U
t:34 - cmnm5U


PDB Structures:


1XZP

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

TrmE is a 50 kDa guanine nucleotide-binding protein conserved between bacteria and man. It is involved in the modification of uridine bases (U34) at the first anticodon (wobble) position of tRNAs decoding two-family box triplets. The precise role of TrmE in the modification reaction is hitherto unknown. Here, we report the X-ray structure of TrmE from Thermotoga maritima. The structure reveals a three-domain protein comprising the N-terminal alpha/beta domain, the central helical domain and the G domain, responsible for GTP binding and hydrolysis. The N-terminal domain induces dimerization and is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase. Biochemical and structural studies show that TrmE indeed binds formyl-tetrahydrofolate. A cysteine residue, necessary for modification of U34, is located close to the C1-group donor 5-formyl-tetrahydrofolate, suggesting a direct role of TrmE in the modification analogous to DNA modification enzymes. We propose a reaction mechanism whereby TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate.

Download RCSB-PDB Structures:

Pdb Files   1XZP.pdb   1XZQ.pdb  
Pdbx/mmCIF Files   1XZP.cif   1XZQ.cif  


Protein sequence:

MDTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGKMDLTSAEAVRDLIEAKSETSLKLSLRNLKGGLRDFVDSLRRELIEVLAEIRVELDYPDEIETNTGEVVTRLERIKEKLTEELKKADAGILLNRGLRMVIVGKPNVGKSTLLNRLLNEDRAIVTDIPGTTRDVISEEIVIRGILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEEDRKILERIKNKRYLVVINKVDVVEKINEEEIKNKLGTDRHMVKISALKGEGLEKLEESIYRETQEIFERGSDSLITNLRQKQLLENVKGHLEDAIKSLKEGMPVDMASIDLERALNLLDEVTGRSFREDLLDTIFSNFCVGK

Comments:

Homologue of E. coli MnmE. Hydrolyses GTP. MnmE works in complex with MnmG (GidA). Catalyzes two independent reactions according to substrate (glycine or ammonium).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
Um:cmnm5Um tRNA (t)   34
s2U:nm5s2U tRNA (t)   34
se2U:nm5se2U tRNA (t)   34
s2U:cmnm5s2U tRNA (t)   34
se2U:cmnm5se2U tRNA (t)   34
U:nm5U tRNA (t)   34
U:cmnm5U tRNA (t)   34

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M D T I V A V A T P P G K G A I A I L R L S G P D S W K I V Q K H L R T R S K I V P R K A I H G W I H E N G E D V D E V V V V F Y K S P K S Y T G E D M V E V M C H G G P L V V K K L L D L F L K S G A R M A E P G E F T K R A F L N G K M D L T S A E A V R D L I E A K S E T S L K L S L R N L K G G L R D F V D S L R R E L I E V L A E I R V E L D Y P D E I E T N T G E V V T R L E R I K E K L T E E L K K A D A G I L L N R G L R M V I V G K P N V G K S T L L N R L L N E D R A I V T D I P G T T R D V I S E E I V I R G I L F R I V D T A G V R S E T N D L V E R L G I E R T L Q E I E K A D I V L F V L D A S S P L D E E D R K I L E R I K N K R Y L V V I N K V D V V E K I N E E E I K N K L G T D R H M V K I S A L K G E G L E K L E E S I Y R E T Q E I F E R G S D S L I T N L R Q K Q L L E N V K G H L E D A I K S L K E G M P V D M A S I D L E R A L N L L D E V T G R S F R E D L L D T I F S N F C V G 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-Q9WYA4-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9WYA4-F1.cif  
DSSP Secondary Structures   Q9WYA4.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The structure of the TrmE GTP-binding protein and its implications for tRNA modification. Scrima A, Vetter IR, Armengod ME, Wittinghofer A EMBO J [details] 15616586 -
Characterization of GTPase activity of TrmE, a member of a novel GTPase superfamily, from Thermotoga maritima. Yamanaka K, Hwang J, Inouye M J Bacteriol [details] 11092873 -
Enzymology of tRNA modification in the bacterial MnmEG pathway. Armengod ME, Moukadiri I, Prado S, Ruiz-Partida R, Benitez-Paez A, Villarroya M, Lomas R, Garzon MJ, Martinez-Zamora A, Meseguer S, Navarro-Gonzalez C Biochimie [details] 22386868 -

Links:

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