Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA wybutosine-synthesizing protein 1
GI: 2501612
Orf: YPL207W
COG: COG0731
UniProt: Q08960
Alpha Fold Predicted Structure: AF-Q08960-F1
Enzyme type: methyltransferase
Position of modification - modification: t:37 - yW



Protein sequence:

MDGFRVAGALVVGALTAAYLYFGGRFSIALVIIVGYGIYCNEASGGSQDSQEKLDLNKQQKKPCCSDKKIADGGKKTGGCCSDKKNGGGKGGGCCSSKGGKKGGCCSSKGGKKGGCCSSKKNIGDNENTATEVEKAVNYPVTVDFTEVFRKPTKKRSSTPKVFSKNSSSNSRVGKKLSVSKKIGPDGLIKSALTISNETLLSSQIYVLYSSLQGAASKAAKSVYDKLKELDELTNEPKLLNLDDLSDFDDYFINVPVENALYVLVLPSYDIDCPLDYFLQTLEENANDFRVDSFPLRKLVGYTVLGLGDSESWPEKFCYQAKRADHWISRLGGRRIFPLGKVCMKTGGSAKIDEWTSLLAETLKDDEPIIYEYDENADSEEDEEEGNGSDELGDVEDIGGKGSNGKFSGADEIKQMVAKDSPTYKNLTKQGYKVIGSHSGVKICRWTKNELRGKGSCYKKSLFNIASSRCMELTPSLACSSKCVFCWRHGTNPVSKNWRWEVDEPEYILENALKGHYSMIKQMRGVPGVIAERFAKAFEVRHCALSLVGEPILYPHINKFIQLLHQKGITSFLVCNAQHPEALRNIVKVTQLYVSIDAPTKTELKKVDRPLYKDFWERMVECLEILKTVQNHQRTVFRLTLVKGFNMGDVSAYADLVQRGLPGFIEVKGATFSGSSDGNGNPLTMQNIPFYEECVKFVKAFTTELQRRGLHYDLAAEHAHSNCLLIADTKFKINGEWHTHIDFDKFFVLLNSGKDFTYMDYLEKTPEWALFGNGGFAPGNTRVYRKDKKKQNKENQETTTRETPLPPIPA

Comments:

An Fe-S cluster protein, *may* catalyze tricyclic formation of yW using Ado-Met and FMN as cofactors. Radical SAM enzyme.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
m1G:imG-14 RNA tRNA 37 #AA #AA tRNAPhe#AA Endoplasmic reticulum

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M D G F R V A G A L V V G A L T A A Y L Y F G G R F S I A L V I I V G Y G I Y C N E A S G G S Q D S Q E K L D L N K Q Q K K P C C S D K K I A D G G K K T G G C C S D K K N G G G K G G G C C S S K G G K K G G C C S S K G G K K G G C C S S K K N I G D N E N T A T E V E K A V N Y P V T V D F T E V F R K P T K K R S S T P K V F S K N S S S N S R V G K K L S V S K K I G P D G L I K S A L T I S N E T L L S S Q I Y V L Y S S L Q G A A S K A A K S V Y D K L K E L D E L T N E P K L L N L D D L S D F D D Y F I N V P V E N A L Y V L V L P S Y D I D C P L D Y F L Q T L E E N A N D F R V D S F P L R K L V G Y T V L G L G D S E S W P E K F C Y Q A K R A D H W I S R L G G R R I F P L G K V C M K T G G S A K I D E W T S L L A E T L K D D E P I I Y E Y D E N A D S E E D E E E G N G S D E L G D V E D I G G K G S N G K F S G A D E I K Q M V A K D S P T Y K N L T K Q G Y K V I G S H S G V K I C R W T K N E L R G K G S C Y K K S L F N I A S S R C M E L T P S L A C S S K C V F C W R H G T N P V S K N W R W E V D E P E Y I L E N A L K G H Y S M I K Q M R G V P G V I A E R F A K A F E V R H C A L S L V G E P I L Y P H I N K F I Q L L H Q K G I T S F L V C N A Q H P E A L R N I V K V T Q L Y V S I D A P T K T E L K K V D R P L Y K D F W E R M V E C L E I L K T V Q N H Q R T V F R L T L V K G F N M G D V S A Y A D L V Q R G L P G F I E V K G A T F S G S S D G N G N P L T M Q N I P F Y E E C V K F V K A F T T E L Q R R G L H Y D L A A E H A H S N C L L I A D T K F K I N G E W H T H I D F D K F F V L L N S G K D F T Y M D Y L E K T P E W A L F G N G G F A P G N T R V Y R K D K K K Q N K E N Q E T T T R E T P L P P I P 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-Q08960-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q08960-F1.cif  
DSSP Secondary Structures   Q08960.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 -
Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. Waas WF, de Crecy-Lagard V, Schimmel P J Biol Chem [details] 16162496 -
Radical mediated ring formation in the biosynthesis of the hypermodified tRNA base wybutosine. Young AP, Bandarian V... Curr Opin Chem Biol [details] 23856057 -

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