Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA uridine(34) 5-carboxymethylaminomethyl synthesis GTPase
Synonym: ThdF, TrmE
GI: 2851487
Orf: b3706
COG: COG0486
UniProt: P25522
Structures: | 2GJ8 | 2GJ9 | 2GJA |
Alpha Fold Predicted Structure: AF-P25522-F1
Complex: MnmE/MnmG
Enzyme type: GTPase
Position of modification - modification: t:34 - cmnm5s2U
t:34 - mnm5s2U
t:34 - cmnm5Um
t:34 - mnm5U


PDB Structures:


2GJ8

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

MnmE, a Guanine nucleotide-binding protein conserved between bacteria and man, is involved in the modification of tRNAs. Here we provide biochemical and X-ray structural evidence for a new GTP-hydrolysis mechanism, where the G-domains of MnmE dimerise in a potassium-dependent manner and induce GTP hydrolysis. The structure in the presence of GDP-AlFx and potassium shows how juxtaposition of the subunits induces a conformational change around the nucleotide which reorients the catalytic machinery. A critical glutamate is positioned such as to stabilise or activate the attacking water. Potassium provides a positive charge into the catalytic site in a position analogous to the arginine finger in the Ras-RasGAP system. Mutational studies show that potassium-dependent dimerisation and GTP hydrolysis can be uncoupled and that interaction between the G-domains is a prerequisite for subsequent phosphoryl transfer. We propose a model for the juxtaposition of G-domains in the full-length protein and how it induces conformational changes in the putative tRNA-modification centre.

Download RCSB-PDB Structures:

Pdb Files   2GJ8.pdb   2GJ9.pdb   2GJA.pdb  
Pdbx/mmCIF Files   2GJ8.cif   2GJ9.cif   2GJA.cif  


Protein sequence:

MSDNDTIVAQATPPGRGGVGILRISGFKAREVAETVLGKLPKPRYADYLPFKDADGSVLDQGIALWFPGPNSFTGEDVLELQGHGGPVILDLLLKRILTIPGLRIARPGEFSERAFLNDKLDLAQAEAIADLIDASSEQAARSALNSLQGAFSARVNHLVEALTHLRIYVEAAIDFPDEEIDFLSDGKIEAQLNDVIADLDAVRAEARQGSLLREGMKVVIAGRPNAGKSSLLNALAGREAAIVTDIAGTTRDVLREHIHIDGMPLHIIDTAGLREASDEVERIGIERAWQEIEQADRVLFMVDGTTTDAVDPAEIWPEFIARLPAKLPITVVRNKADITGETLGMSEVNGHALIRLSARTGEGVDVLRNHLKQSMGFDTNMEGGFLARRRHLQALEQAAEHLQQGKAQLLGAWAGELLAEELRLAQQNLSEITGEFTSDDLLGRIFSSFCIGK

Comments:

Proteins MnmE and MnmG (formerly TrmE and GidA, respectively) are evolutionarily conserved from bacteria to eukaryotic organelles. MnmE and MnmG are dimeric and form a functional α2β2 heterotetrameric complex (MnmEG) in which both proteins are interdependent. MnmE is a GTP- and tetrahydrofolate (THF)-binding protein, whereas MnmG is a FAD- and NADH-binding protein. The MnmEG complex catalyzes the addition of the aminomethyl (nm) and carboxymethylaminomethyl (cmnm) groups to position 5 of the wobble uridine using ammonium and glycine, respectively. Both reactions require GTP and FAD as well as NADH if FAD is limiting in the in vitro reaction. Hydrolyses GTP (contains a P-loop domain). MnmE works as a dimer in complex with MnmG (GidA, also a dimer). MnmEG complex catalyzes two different reactions depending on the substrate (glycine or ammonium). The choice between glycine and ammonium was shown to be influenced by the growth phase and medium with the glycine pathway being chosen in the minimal medium and in the exponential phase. However, in the case of tRNAGln cmnm5s2U the glycine pathway is always the dominant one and for tRNALeu cmnm5Um the ammonium pathway was observed only in vitro. MnmE has been shown to negatively regulate the activity of MiaB involved in methylthiolation of i6A37 of tRNA. Crystal structures are available only for the G-domain. The homologue from P. aeruginosa has been crystallized. The resulting modification plays a critical role in decoding NNG/A codons and reading-frame maintenance during mRNA translation (Moukadiri et al. 2009 ). The xm5 modification seems to be critical for decoding NNG/A codons by stabilizing U•G pairing at the wobble position as well as improving the reading of the NNA codons (Kurata et al. 2008). Moreover, the lack of these modifications produces translational frameshifting and a pleiotropic phenotype in bacteria (Björk et al. 2014), whereas it has been associated with mitochondrial encephalomyopathies in humans (Kirino et al. 2005). The yeast mitochondrial homolog is Mss1, working in a complex with Mto1.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:cmnm5U RNA tRNA 34 UUU !UU tRNALysUUU wobble - position Prokaryotic Cytosol 24293650   
U:nm5U RNA tRNA 34 UUU ∪UU tRNALysUUU wobble - position Prokaryotic Cytosol 24293650   
Um:cmnm5Um RNA tRNA 34 JAA )AA tRNALeuJAA wobble - position Prokaryotic Cytosol 24293650   
s2U:nm5s2U RNA tRNA 34 2UU ∫UU tRNALys2UU wobble - position Prokaryotic Cytosol 24293650   
se2U:nm5se2U tRNA (t)   34
s2U:cmnm5s2U RNA tRNA 34 2UU $UU tRNALys2UU wobble - position Prokaryotic Cytosol 24293650   
se2U:cmnm5se2U tRNA (t)   34
s2U:cmnm5s2U RNA tRNA 34 2UC $UC tRNAGlu2UC wobble - position Prokaryotic Cytosol 24293650   
s2U:cmnm5s2U RNA tRNA 34 2UG $UG tRNAGln2UG wobble - position Prokaryotic Cytosol 24293650   
U:cmnm5U RNA tRNA 34 UUC !UC tRNAGluUUC wobble - position Prokaryotic Cytosol 24293650   
s2U:nm5s2U RNA tRNA 34 2UC ∫UC tRNAGlu∫UC wobble - position Prokaryotic Cytosol 24293650   
U:nm5U RNA tRNA 34 UUC ∪UC tRNAGluUUC wobble - position Prokaryotic Cytosol 24293650   
U:cmnm5U RNA tRNA 34 UUG !UG tRNAGlnUUG wobble - position Prokaryotic Cytosol 24293650   
s2U:nm5s2U RNA tRNA 34 2UG ∫UG tRNAGln2UG wobble - position Prokaryotic Cytosol 24293650   
U:nm5U RNA tRNA 34 UUG ∫UG tRNAGlnUUG wobble - position Prokaryotic Cytosol 24293650   
U:nm5U RNA tRNA 34 UAA ∪AA tRNALeuUAA wobble - position Prokaryotic Cytosol 24293650   
U:cmnm5U RNA tRNA 34 UAA !AA tRNALeuUAA wobble - position Prokaryotic Cytosol 24293650   
U:nm5U RNA tRNA 34 UCU ∫CU tRNAArgUCU wobble - position Prokaryotic Cytosol 24293650   
U:cmnm5U RNA tRNA 34 UCU !CU tRNAArgUCU wobble - position Prokaryotic Cytosol 24293650   
U:nm5U RNA tRNA 34 UCC ∪CC tRNAGlyUCC wobble - position Prokaryotic Cytosol 24293650   
U:cmnm5U RNA tRNA 34 UCC $CC tRNAGlyUCC wobble - position Prokaryotic Cytosol 24293650   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S D N D T I V A Q A T P P G R G G V G I L R I S G F K A R E V A E T V L G K L P K P R Y A D Y L P F K D A D G S V L D Q G I A L W F P G P N S F T G E D V L E L Q G H G G P V I L D L L L K R I L T I P G L R I A R P G E F S E R A F L N D K L D L A Q A E A I A D L I D A S S E Q A A R S A L N S L Q G A F S A R V N H L V E A L T H L R I Y V E A A I D F P D E E I D F L S D G K I E A Q L N D V I A D L D A V R A E A R Q G S L L R E G M K V V I A G R P N A G K S S L L N A L A G R E A A I V T D I A G T T R D V L R E H I H I D G M P L H I I D T A G L R E A S D E V E R I G I E R A W Q E I E Q A D R V L F M V D G T T T D A V D P A E I W P E F I A R L P A K L P I T V V R N K A D I T G E T L G M S E V N G H A L I R L S A R T G E G V D V L R N H L K Q S M G F D T N M E G G F L A R R R H L Q A L E Q A A E H L Q Q G K A Q L L G A W A G E L L A E E L R L A Q Q N L S E I T G E F T S D D L L G R I F S S 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-P25522-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P25522-F1.cif  
DSSP Secondary Structures   P25522.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties. Cabedo H, Macian F, Villarroya M, Escudero JC, Martinez-Vicente M, Knecht E, Armengod ME EMBO J [details] 10601028 -
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 -
Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element. Scrima A, Wittinghofer A EMBO J [details] 16763562 -
Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions. Moukadiri I, Prado S, Piera J, Velázquez-Campoy A, Björk GR, Armengod ME Nucleic Acids Res [details] 19767610 -
Overexpression, crystallization and preliminary X-ray crystallographic analysis of Pseudomonas aeruginosa MnmE, a GTPase involved in tRNA modification. Lee HH, Suh SW Acta Crystallogr Sect F Struct Biol Cryst Commun [details] 20693664 -
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 -
The output of the tRNA modification pathways controlled by the Escherichia coli MnmEG and MnmC enzymes depends on the growth conditions and the tRNA species. Moukadiri I, Garzon MJ, Bjork GR, Armengod ME... Nucleic Acids Res [details] 24293650 -
SAXS analysis of the tRNA-modifying enzyme complex MnmE/MnmG reveals a novel interaction mode and GTP-induced oligomerization. Fislage M, Brosens E, Deyaert E, Spilotros A, Pardon E, Loris R, Steyaert J, Garcia-Pino A, Versees W... Nucleic Acids Res [details] 24634441 -

Links:

_EcoCyc_
_PubMed_