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: Crystal Structure of E.coli MnmG (GidA), a Highly-Conserved tRNA Modifying Enzyme
Classification: RNA BINDING PROTEIN
Technique: X-Ray Diffraction
Resolution: 2.41
R value free: 0.238
R value observed: 0.203
R value work: 0.201

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 ) .





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
50100150200250300350400450500550600SequenceGHTBSN

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:

Links:

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