Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA uridine(34) 5-carboxymethylaminomethyl synthesis enzyme
Synonym: GidA, TrmF
GI: 62288115
Orf: b3741
COG: COG0445
UniProt: P0A6U3
Structures: | 3CP2 | 3CES |
Alpha Fold Predicted Structure: AF-P0A6U3-F1
Complex: MnmG/MnmE
Enzyme type: other
Position of modification - modification: t:34 - cmnm5s2U
t:34 - mnm5s2U
t:34 - cmnm5Um
t:34 - mnm5U


PDB Structures:


3CP2

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The MnmE-MnmG complex is involved in tRNA modification. We have determined the crystal structure of Escherichia coli MnmG at 2.4-A resolution, mutated highly conserved residues with putative roles in flavin adenine dinucleotide (FAD) or tRNA binding and MnmE interaction, and analyzed the effects of these mutations in vivo and in vitro. Limited trypsinolysis of MnmG suggests significant conformational changes upon FAD binding.

Download RCSB-PDB Structures:

Pdb Files   3CES.pdb   3CP2.pdb  
Pdbx/mmCIF Files   3CES.cif   3CP2.cif  


Protein sequence:

MFYPDPFDVIIIGGGHAGTEAAMAAARMGQQTLLLTHNIDTLGQMSCNPAIGGIGKGHLVKEVDALGGLMAKAIDQAGIQFRILNASKGPAVRATRAQADRVLYRQAVRTALENQPNLMIFQQAVEDLIVENDRVVGAVTQMGLKFRAKAVVLTVGTFLDGKIHIGLDNYSGGRAGDPPSIPLSRRLRELPLRVGRLKTGTPPRIDARTIDFSVLAQQHGDNPMPVFSFMGNASQHPQQVPCYITHTNEKTHDVIRSNLDRSPMYAGVIEGVGPRYCPSIEDKVMRFADRNQHQIFLEPEGLTSNEIYPNGISTSLPFDVQMQIVRSMQGMENAKIVRPGYAIEYDFFDPRDLKPTLESKFIQGLFFAGQINGTTGYEEAAAQGLLAGLNAARLSADKEGWAPARSQAYLGVLVDDLCTLGTKEPYRMFTSRAEYRLMLREDNADLRLTEIGRELGLVDDERWARFNEKLENIERERQRLKSTWVTPSAEAAAEVNAHLTAPLSREASGEDLLRRPEMTYEKLTTLTPFAPALTDEQAAEQVEIQVKYEGYIARQQDEIEKQLRNENTLLPATLDYRQVSGLSNEVIAKLNDHKPASIGQASRISGVTPAAISILLVWLKKQGMLRRSA

Comments:

Proteins MnmE and MnmG are evolutionary 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. MnmG is a FAD- and NADH-binding protein, while instead, MnmE is a GTP- and tetrahydrofolate (THF)-binding protein. The MnmEG heterotetrameric complex catalyzes the addition of the aminomethyl (nm) and carboxymethylaminomethyl (cmnm) groups to position 5 of the wobble uridine using ammonium and glycine, respectively. In E.coli MnmEG complex is involved in the modification of the wobble uridine of tRNALysmnm5s2UUU, tRNAGlncmnm5s2UUG, tRNAArgmnm5UCU, tRNAGlumnm5s2UUC, tRNALeucmnm5UmAA, tRNAGlymnm5UCC. MNMEG modified substrates are neither the starting nor the final products of the catalytic pathway. Indeed, MnmA is involved in the 2-thiolation of the wobble uridine after which MnmEG complex is involved (Moukadiri et al. 2014 ) .




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
s2U:cmnm5s2U RNA tRNA 34 2UU $UU tRNALys2UU wobble - position Prokaryotic Cytosol 24293650   
s2U:nm5s2U RNA tRNA 34 2UU ∫UU tRNALys2UU wobble - position Prokaryotic Cytosol 24293650   
s2U:nm5s2U RNA tRNA 34 2UC ∫UC tRNAGlu2UC wobble - position Prokaryotic Cytosol 24293650   
s2U:cmnm5s2U RNA tRNA 34 2UC $UC tRNAGlu2UC wobble - position Prokaryotic Cytosol 24293650   
s2U:nm5s2U RNA tRNA 34 2UG ∫UG tRNAGln2UG wobble - position Prokaryotic Cytosol 24293650   
s2U:cmnm5s2U RNA tRNA 34 2UG $UG tRNAGln2UG wobble - position Prokaryotic Cytosol 24293650   
s2U:nm5s2U RNA tRNA 34 2AA ∫AA tRNALeu2AA wobble - position Prokaryotic Cytosol 24293650   
s2U:cmnm5s2U RNA tRNA 34 2AA $AA tRNALeu2AA wobble - position Prokaryotic Cytosol 24293650   
s2U:nm5s2U RNA tRNA 34 2CU ∫CU tRNAArg2CU wobble - position Prokaryotic Cytosol 24293650   
s2U:cmnm5s2U RNA tRNA 34 2CU $CU tRNAArg2CU wobble - position Prokaryotic Cytosol 24293650   
s2U:nm5s2U RNA tRNA 34 2CC ∫CC tRNAGly2CC wobble - position Prokaryotic Cytosol 24293650   
s2U:cmnm5s2U RNA tRNA 34 2CC $CC tRNAGly2CC wobble - position Prokaryotic Cytosol 24293650   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P0A6U3-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0A6U3-F1.cif  
DSSP Secondary Structures   P0A6U3.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli. Yim L, Moukadiri I, Bjork GR, Armengod ME Nucleic Acids Res [details] 17062623 -
Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate. Meyer S, Scrima A, Versées W, Wittinghofer A J Mol Biol [details] 18565343 -
Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. Brégeon D, Colot V, Radman M, Taddei F Genes Dev [details] 11544186 -
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 -
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 -

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