Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA modification GTPase MnmE
Synonym: TrmE
GI: 17232169
COG: COG0486
UniProt: Q8YN91
Structures: | 3GEH |
Alpha Fold Predicted Structure: AF-Q8YN91-F1
Complex: MnmE/MnmG
Enzyme type: GTPase
Position of modification - modification: t:34 - cmnm5s2U
t:34 - cmnm5U


PDB Structures:


3GEH

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

MnmE, which is involved in the modification of the wobble position of certain tRNAs, belongs to the expanding class of G proteins activated by nucleotide-dependent dimerization (GADs). Previous models suggested the protein to be a multidomain protein whose G domains contact each other in a nucleotide dependent manner. Here we employ a combined approach of X-ray crystallography and pulse electron paramagnetic resonance (EPR) spectroscopy to show that large domain movements are coupled to the G protein cycle of MnmE. The X-ray structures show MnmE to be a constitutive homodimer where the highly mobile G domains face each other in various orientations but are not in close contact as suggested by the GDP-AlF(x) structure of the isolated domains. Distance measurements by pulse double electron-electron resonance (DEER) spectroscopy show that the G domains adopt an open conformation in the nucleotide free/GDP-bound and an open/closed two-state equilibrium in the GTP-bound state, with maximal distance variations of 18 A. With GDP and AlF(x), which mimic the transition state of the phosphoryl transfer reaction, only the closed conformation is observed. Dimerization of the active sites with GDP-AlF(x) requires the presence of specific monovalent cations, thus reflecting the requirements for the GTPase reaction of MnmE. Our results directly demonstrate the nature of the conformational changes MnmE was previously suggested to undergo during its GTPase cycle. They show the nucleotide-dependent dynamic movements of the G domains around two swivel positions relative to the rest of the protein, and they are of crucial importance for understanding the mechanistic principles of this GAD.

Download RCSB-PDB Structures:

Pdb Files   3GEH.pdb  
Pdbx/mmCIF Files   3GEH.cif  


Protein sequence:

MAITGTIAAIATAIVPQQGSVGIVRVSGSQAIAIAQTLFDAPGKQVWESHRILYGYIRHPQTRQIVDEALLLLMKAPRSYTREDVVEFHCHGGIIAVQQVLQLCLESGARLAQPGEFTLRAFLNGRLDLTQAESIADLVGARSPQAAQTALAGLQGKLAHPIRQLRANCLDILAEIEARIDFEEDLPPLDDEAIISDIENIAAEISQLLATKDKGELLRTGLKVAIVGRPNVGKSSLLNAWSQSDRAIVTDLPGTTRDVVESQLVVGGIPVQVLDTAGIRETSDQVEKIGVERSRQAANTADLVLLTIDAATGWTTGDQEIYEQVKHRPLILVMNKIDLVEKQLITSLEYPENITQIVHTAAAQKQGIDSLETAILEIVQTGKVQAADMDLAINQRQAAALTQAKMSLEQVQATITQQLPLDFWTIDLRGAIQALGEITGEEVTESVLDRIFSRFCIGK

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). Crystal structures available only for the G-domain.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
Um:cmnm5Um tRNA (t)   34 19806182   
s2U:nm5s2U tRNA (t)   34 19806182   
se2U:nm5se2U tRNA (t)   34 19806182   
s2U:cmnm5s2U tRNA (t)   34 19806182   
se2U:cmnm5se2U tRNA (t)   34 19806182   
U:nm5U tRNA (t)   34 19806182   
U:cmnm5U tRNA (t)   34 19806182   

Alpha Fold Predicted Structure:






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Protein sequence:

M A I T G T I A A I A T A I V P Q Q G S V G I V R V S G S Q A I A I A Q T L F D A P G K Q V W E S H R I L Y G Y I R H P Q T R Q I V D E A L L L L M K A P R S Y T R E D V V E F H C H G G I I A V Q Q V L Q L C L E S G A R L A Q P G E F T L R A F L N G R L D L T Q A E S I A D L V G A R S P Q A A Q T A L A G L Q G K L A H P I R Q L R A N C L D I L A E I E A R I D F E E D L P P L D D E A I I S D I E N I A A E I S Q L L A T K D K G E L L R T G L K V A I V G R P N V G K S S L L N A W S Q S D R A I V T D L P G T T R D V V E S Q L V V G G I P V Q V L D T A G I R E T S D Q V E K I G V E R S R Q A A N T A D L V L L T I D A A T G W T T G D Q E I Y E Q V K H R P L I L V M N K I D L V E K Q L I T S L E Y P E N I T Q I V H T A A A Q K Q G I D S L E T A I L E I V Q T G K V Q A A D M D L A I N Q R Q A A A L T Q A K M S L E Q V Q A T I T Q Q L P L D F W T I D L R G A I Q A L G E I T G E E V T E S V L D R I F S R F C I 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-Q8YN91-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q8YN91-F1.cif  
DSSP Secondary Structures   Q8YN91.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy. Meyer S, Bohme S, Kruger A, Steinhoff HJ, Klare JP, Wittinghofer A PLoS Biol [details] 19806182 -
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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