Modomics - A Database of RNA Modifications

ID Card:

Full name: MnmD tRNA methyltransferase
Synonym: MnmC2
GI: 15606976
Orf: aq_1980
COG: COG752
UniProt: O67789
Structures: | 3VYW |
Alpha Fold Predicted Structure: AF-O67789-F1
Enzyme type: methyltransferase
Position of modification - modification: t:34 - mnm5s2U
t:34 - mnm5U


PDB Structures:


3VYW

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Post-transcriptional modifications of the wobble uridine (U34) of tRNAs play a critical role in reading NNA/G codons belonging to split codon boxes. In a subset of Escherichia coli tRNA, this wobble uridine is modified to 5-methylaminomethyluridine (mnm(5)U34) through sequential enzymatic reactions. Uridine 34 is first converted to 5-carboxymethylaminomethyluridine (cmnm(5)U34) by the MnmE-MnmG enzyme complex. The cmnm(5)U34 is further modified to mnm(5)U by the bifunctional MnmC protein. In the first reaction, the FAD-dependent oxidase domain (MnmC1) converts cmnm(5)U into 5-aminomethyluridine (nm(5)U34), and this reaction is immediately followed by the methylation of the free amino group into mnm(5)U34 by the S-adenosylmethionine-dependent domain (MnmC2). Aquifex aeolicus lacks a bifunctional MnmC protein fusion and instead encodes the Rossmann-fold protein DUF752, which is homologous to the methyltransferase MnmC2 domain of Escherichia coli MnmC (26% identity). Here, we determined the crystal structure of the A. aeolicus DUF752 protein at 2.5 Å resolution, which revealed that it catalyzes the S-adenosylmethionine-dependent methylation of nm(5)U in vitro, to form mnm(5)U34 in tRNA. We also showed that naturally occurring tRNA from A. aeolicus contains the 5-mnm group attached to the C5 atom of U34. Taken together, these results support the recent proposal of an alternative MnmC1-independent shortcut pathway for producing mnm(5)U34 in tRNAs.

Download RCSB-PDB Structures:

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


Protein sequence:

MKREEYLKNYLESYLRKKEVSLTEEEFNVILREFLRFAYNPEESGQEIADTADGSKTLIHKTYGEPYHSQTAGAIRESLYKFVRPSRILEKAKERKVIRILDVGFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEGERLSLKVLLGDARKRIKEVENFKADAVFHDAFSPYKNPELWTLDFLSLIKERIDEKGYWVSYSSSLSVRKSLLTLGFKVGSSREIGRKRKGTVASLKAPVPPMEENEVRKLVLSPFAVPMRDEKLDKEPLEILIDYLLKVYKISR

Comments:

In E.coli (and many other bacteria) MnmCD it is a bifunctional enzyme, composed of two domains that catalyze two successive reactions at the uridine wobble position 34 in tRNA: first a deacetylation reaction of cmnm5U into nm5U, then methylation of the amine group of nm5U to form mnm5U. In other organisms they may be unlinked (separate proteins), then identified as MnmC for the deacetylase and MnmD for the methylase. In certain bacteria, the catalytic domain for the deacetylation reaction is absent in their genome and only the gene coding for MnmD is present. In other bacteria, MnmC and MnmD are both present.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
nm5U:mnm5U tRNA (t) 34 23091054   
nm5s2U:mnm5s2U tRNA (t) 34 23091054   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-O67789-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O67789-F1.cif  
DSSP Secondary Structures   O67789.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1). Kitamura A, Nishimoto M, Sengoku T, Shibata R, Jager G, Bjork GR, Grosjean H, Yokoyama S, Bessho Y... J Biol Chem [details] 23091054 -

Links:

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