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: Structure of the GTP-binding protein TrmE from Thermotoga maritima
Classification: HYDROLASE
Technique: X-Ray Diffraction
Resolution: 2.3
R value free: 0.252
R value observed: 0.227
R value work: 0.226

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).





Alpha Fold Predicted Structure:




Parsing response... [411069/411069]


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
50100150200250300350400450SequenceHTBSN

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:

Links:

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