Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA 2-thiocytidine(32) synthetase
Synonym: YdaO
GI: 2495598
Orf: b1344
COG: COG0037
UniProt: P76055
Alpha Fold Predicted Structure: AF-P76055-F1
Enzyme type: thiolase
Position of modification - modification: t:32 - s2C



Protein sequence:

MQENQQITKKEQYNLNKLQKRLRRNVGEAIADFNMIEEGDRIMVCLSGGKDSYTMLEILRNLQQSAPINFSLVAVNLDQKQPGFPEHVLPEYLEKLGVEYKIVEENTYGIVKEKIPEGKTTCSLCSRLRRGILYRTATELGATKIALGHHRDDILQTLFLNMFYGGKMKGMPPKLMSDDGKHIVIRPLAYCREKDIQRFADAKAFPIIPCNLCGSQPNLQRQVIADMLRDWDKRYPGRIETMFSAMQNVVPSHLCDTNLFDFKGITHGSEVVNGGDLAFDREEIPLQPACWQPEEDENQLDELRLNVVEVK

Comments:

The synthesis of s2C requires IscS as a sulfur donor and belongs to the “iron-cluster” pathway (as MiaB). Much sequence similarities exist between bacterial TtcA and yeast Tuc1 responsible for the thiolation of s2U34 (convergent evolution). They might have evolved from a common thiolase precursor.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:s2C RNA tRNA 32 ICG ICG tRNAArgICG anticodon-loop Prokaryotic Cytosol
C:s2C RNA tRNA 32 CCG CCG tRNAArgCCG anticodon-loop Prokaryotic Cytosol
C:s2C RNA tRNA 32 {CU {CU tRNAArg{CU anticodon-loop Prokaryotic Cytosol
C:s2C RNA tRNA 32 GCU GCU tRNASerGCU anticodon-loop Prokaryotic Cytosol

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P76055-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P76055-F1.cif  
DSSP Secondary Structures   P76055.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The conserved Cys-X1-X2-Cys motif present in the TtcA protein is required for the thiolation of cytidine in position 32 of tRNA from Salmonella enterica serovar Typhimurium. Jager G, Leipuviene R, Pollard MG, Qian Q, Bjork GR J Bacteriol [details] 14729701 -
Iron-sulfur cluster biosynthesis in bacteria: Mechanisms of cluster assembly and transfer. Fontecave M, Ollagnier-de-Choudens S Arch Biochem Biophys [details] 18191630 -
A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast. Bjork GR, Huang B, Persson OP, Bystrom AS RNA [details] 17592039 -
TtcA a new tRNA-thioltransferase with an Fe-S cluster. Bouvier D, Labessan N, Clemancey M, Latour JM, Ravanat JL, Fontecave M, Atta M... Nucleic Acids Res [details] 24914049 -

Links:

_EcoCyc_