Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA 5-methoxyuridine(34) synthase
Synonym: YecP
GI: 3025152
Orf: b1871
COG: COG2230
UniProt: P76291
Structures: | 4QNX | 4QNU | 4QNV |
Alpha Fold Predicted Structure: AF-P76291-F1
Enzyme type: carboxymethyltransferase
Position of modification - modification: t:34 - cmo5U
t:34 - mcmo5U


PDB Structures:


4QNX

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Enzyme-mediated modifications at the wobble position of tRNAs are essential for the translation of the genetic code. We report the genetic, biochemical and structural characterization of CmoB, the enzyme that recognizes the unique metabolite carboxy-S-adenosine-L-methionine (Cx-SAM) and catalyzes a carboxymethyl transfer reaction resulting in formation of 5-oxyacetyluridine at the wobble position of tRNAs. CmoB is distinctive in that it is the only known member of the SAM-dependent methyltransferase (SDMT) superfamily that utilizes a naturally occurring SAM analog as the alkyl donor to fulfill a biologically meaningful function. Biochemical and genetic studies define the in vitro and in vivo selectivity for Cx-SAM as alkyl donor over the vastly more abundant SAM. Complementary high-resolution structures of the apo- and Cx-SAM bound CmoB reveal the determinants responsible for this remarkable discrimination. Together, these studies provide mechanistic insight into the enzymatic and non-enzymatic feature of this alkyl transfer reaction which affords the broadened specificity required for tRNAs to recognize multiple synonymous codons.

Download RCSB-PDB Structures:

Pdb Files   4QNU.pdb   4QNV.pdb   4QNX.pdb  
Pdbx/mmCIF Files   4QNU.cif   4QNV.cif   4QNX.cif  


Protein sequence:

MIDFGNFYSLIAKNHLSHWLETLPAQIANWQREQQHGLFKQWSNAVEFLPEIKPYRLDLLHSVTAESEEPLSAGQIKRIETLMRNLMPWRKGPFSLYGVNIDTEWRSDWKWDRVLPHLSDLTGRTILDVGCGSGYHMWRMIGAGAHLAVGIDPTQLFLCQFEAVRKLLGNDQRAHLLPLGIEQLPALKAFDTVFSMGVLYHRRSPLEHLWQLKDQLVNEGELVLETLVIDGDENTVLVPGDRYAQMRNVYFIPSALALKNWLKKCGFVDIRIADVSVTTTEEQRRTEWMVTESLADFLDPHDPGKTVEGYPAPKRAVLIARKP

Comments:

CmoB is an S-adenosyl-L-methionine dependent (SAM-dependent) methyltransferase belonging to the COG2230 ortholog gene family. It has been speculated its implication in a tRNA modification pathway where ho5U is modified to cmo5U (Kim et al. 2013 ).

Indeed, it has been observed to modify tRNAPro in a chain of reactions that implies the modification of U34 to ho5U34 by unidentified enzymes and hoU34 to mo5U by CmoB itself a the second step and the final modification of ho5U34 to cmoU34 by CmoA.(Nasvall et al. 2013 ).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
ho5U:mo5U RNA tRNA 34 wobble - position Prokaryotic Cytosol
ho5U:cmo5U RNA tRNA 34 wobble - position Prokaryotic Cytosol 23676670   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P76291-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P76291-F1.cif  
DSSP Secondary Structures   P76291.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo. Nasvall SJ, Chen P, Bjork GR RNA [details] 15383682 -
The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons. Nasvall SJ, Chen P, Bjork GR RNA [details] 17942742 -
A novel link between the biosynthesis of aromatic amino acids and transfer RNA modification in Escherichia coli. Bjork GR J Mol Biol [details] 6160251 -
Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt PC, Jacobson MP, Lee YS, Almo SC... Nature [details] 23676670 -
S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA. Byrne RT, Whelan F, Aller P, Bird LE, Dowle A, Lobley CM, Reddivari Y, Nettleship JE, Owens RJ, Antson AA, Waterman DG... Acta Crystallogr D Biol Crystallogr [details] 23695253 -
Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification. Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, Brown S, Lee YS, Almo SC... Nucleic Acids Res [details] 25855808 -

Links:

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