Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA modification GTPase MnmE
Synonym: ThdF, TrmE
GI: 21674894
COG: COG0486
UniProt: Q8KAS1
Structures: | 3GEE | 3GEI |
Alpha Fold Predicted Structure: AF-Q8KAS1-F1
Complex: MnmE/MnmG
Enzyme type: GTPase
Position of modification - modification: t:34 - cmnm5s2U
t:34 - cmnm5U


PDB Structures:


3GEE

Structure Description:

Title: Crystal structure of MnmE from Chlorobium tepidum in complex with GDP and FOLINIC ACID
Classification: HYDROLASE
Technique: X-Ray Diffraction
Resolution: 2.95
R value free: 0.27
R value observed: 0.234
R value work: 0.232

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   3GEE.pdb   3GEI.pdb  
Pdbx/mmCIF Files   3GEE.cif   3GEI.cif  


Protein sequence:

MSPSDLHLPVPGHPIAAIATPVGVGALAIVRISGAGVLDLADRVFRKVHGSGKLAEAAGYTAHFGRLYDGEEMVDEVIALVFRAPRSFTAEQMVEFTCHGGPVVVGRVLRLMLDNGCRLAEPGEFTRRAFLNGRIDLLQAEAIGEMIHARTESAYRTAVSQMKGDLSVRLGGLREQLIRSCALIELELDFSEEDVEFQSRDELTMQIETLRSEVNRLIDSYQHGRIVSEGVSTVIAGKPNAGKSTLLNTLLGQERAIVSHMPGTTRDYIEECFIHDKTMFRLTDTAGLREAGEEIEHEGIRRSRMKMAEADLILYLLDLGTERLDDELTEIRELKAAHPAAKFLTVANKLDRAANADALIRAIADGTGTEVIGISALNGDGIDTLKQHMGDLVKNLDKLHEASVLVTSLRHYEALRNASDALQNALELIAHESETELIAFELRAALDYVGQITGKVVNEEVLNTIFDKFCIGK

Comments:

Homologue of E. coli MnmE. Hydrolyses GTP (contains a P-loop domain). MnmE works as dimer in complex with MnmG (GidA also as dimer). Catalyzes two independent reactions according to substrate (glycine or ammonium).





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S P S D L H L P V P G H P I A A I A T P V G V G A L A I V R I S G A G V L D L A D R V F R K V H G S G K L A E A A G Y T A H F G R L Y D G E E M V D E V I A L V F R A P R S F T A E Q M V E F T C H G G P V V V G R V L R L M L D N G C R L A E P G E F T R R A F L N G R I D L L Q A E A I G E M I H A R T E S A Y R T A V S Q M K G D L S V R L G G L R E Q L I R S C A L I E L E L D F S E E D V E F Q S R D E L T M Q I E T L R S E V N R L I D S Y Q H G R I V S E G V S T V I A G K P N A G K S T L L N T L L G Q E R A I V S H M P G T T R D Y I E E C F I H D K T M F R L T D T A G L R E A G E E I E H E G I R R S R M K M A E A D L I L Y L L D L G T E R L D D E L T E I R E L K A A H P A A K F L T V A N K L D R A A N A D A L I R A I A D G T G T E V I G I S A L N G D G I D T L K Q H M G D L V K N L D K L H E A S V L V T S L R H Y E A L R N A S D A L Q N A L E L I A H E S E T E L I A F E L R A A L D Y V G Q I T G K V V N E E V L N T I F D K F C I G K
50100150200250300350400450SequenceGHTBSN

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-Q8KAS1-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q8KAS1-F1.cif  
DSSP Secondary Structures   Q8KAS1.dssp  





Publications:

Links:

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