Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA wybutosine-synthesizing protein 2
Synonym: Trm12, YMA5
GI: 2497109
Orf: YML005W
COG: COG2520
UniProt: Q04235
Alpha Fold Predicted Structure: AF-Q04235-F1
Enzyme type: Alpha-amino-alpha-carboxypropyltransferase
Position of modification - modification: t:37 - yW



Protein sequence:

MSDETMPVEFLVSDKRLLKTIKVKLETNGLFVTPIYSDNDNKVIKSSIEDLNHPLAVEINNIAGVKARFHESGNLERSEGHLKHQSNSITEFTKSFLKDHGLANDKIFLSHLLDHLPLKYTIYPPVVLFNNSTVRSFNHPIWQKAFQLKLFDPNEYYRELLCFLSPGKPSKGTSLHPNNRLLTHLAINNPITEADVLRRPFNIQPLYGKLIDDSILDDNDNTLWENPSQEQLNSSIWCKVIQNGVTQIWSPVFTMFSRGNIKEKKRVLTTFPDICNNDVVDLYAGIGYFTFSYLTKGARTLFAFELNPWSVEGLKRGLKANGFNKSGNCHVFQESNEMCVQRLTEFLSQNPGFRLRIRHINLGLLPSSKQGWPLAIKLIYLQGASLEKVTMHIHENVHIDAIEDGSFEKNVIVELDAINESIALIRNRGIKLQFVRSKLERIKTFAPDIWHVCVDVDVIVST

Comments:

TYW2 transfers α-amino-α-carboxypropyl group from Ado-Met to the side chain at the C-7 position of the yW-187 (imG-14) to produce yW-86.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
imG-14:yW-86 RNA tRNA 37 #AA #AA tRNAPhe#AA anticodon-loop Cytoplasm 16642040    16005430   

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-Q04235-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q04235-F1.cif  
DSSP Secondary Structures   Q04235.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. Noma A, Kirino Y, Ikeuchi Y, Suzuki T EMBO J [details] 16642040 -
A novel methyltransferase required for the formation of the hypermodified nucleoside wybutosine in eucaryotic tRNA. Kalhor HR, Penjwini M, Clarke S Biochem Biophys Res Commun [details] 16005430 -

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