Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA N6-threonylcarbamoyladenosine(37) synthesis protein
Synonym: YgjD
GI: 16130960
COG: COG0533
UniProt: P05852
Structures: | 4WQ4 | 4WQ5 | 4YDU | 6Z81 |
Alpha Fold Predicted Structure: AF-P05852-F1
Complex: TsaBDE
Enzyme type: threonylcarbamoyltransferase
Position of modification - modification: t:37 - t6A


PDB Structures:


4WQ4

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The essential and universal N(6)-threonylcarbamoyladenosine (t(6)A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (TsaB), YjeE (TsaE) and YrdC (TsaC) proteins are necessary and sufficient for the in vitro biosynthesis of t(6)A, using tRNA, ATP, L-threonine and bicarbonate as substrates. YrdC synthesizes the short-lived L-threonylcarbamoyladenylate (TCA), and YgjD, YeaZ and YjeE cooperate to transfer the L-threonylcarbamoyl-moiety from TCA onto adenosine at position 37 of substrate tRNA. We determined the crystal structure of the heterodimer YgjD-YeaZ at 2.3 Å, revealing the presence of an unexpected molecule of ADP bound at an atypical site situated at the YgjD-YeaZ interface. We further showed that the ATPase activity of YjeE is strongly activated by the YgjD-YeaZ heterodimer. We established by binding experiments and SAXS data analysis that YgjD-YeaZ and YjeE form a compact ternary complex only in presence of ATP. The formation of the ternary YgjD-YeaZ-YjeE complex is required for the in vitro biosynthesis of t(6)A but not its ATPase activity.

Download RCSB-PDB Structures:

Pdb Files   4WQ4.pdb   4WQ5.pdb   4YDU.pdb   6Z81.pdb  
Pdbx/mmCIF Files   4WQ4.cif   4WQ5.cif   4YDU.cif   6Z81.cif  


Protein sequence:

MRVLGIETSCDETGIAIYDDEKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKESGLTAKDIDAVAYTAGPGLVGALLVGATVGRSLAFAWDVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPLLSKMAAQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRDNGTDDQTRADIARAFEDAVVDTLMIKCKRALDQTGFKRLVMAGGVSANRTLRAKLAEMMKKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGATADLGVSVRPRWPLAELPAA

Comments:

TsaD, the ortholog of eukaryal/archaeal Kae1, is a weak ATPase (produces ADP) and binds A37-containing tRNA. TsaD forms an essential interaction network with TsaB (YeaZ, a paralog of TsaD) and TsaE (YjeE) proteins. Together with TsaC (multiprotein complex), ATP, threonine and bicarbonate as cofactors, they catalyze the in vitro formation of t6A (threonyl-carbamoylation) at position 37 of bacterial tRNA decoding ANN codons (ile, Met, Thr, Lys, Asn, Ser and Arg).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:t6A RNA tRNA 37 GGC GGC tRNAAlaGGC Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TGC TGC tRNAAlaTGC Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 ACG ACG tRNAArgACG Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GTT GTT tRNAAsnGTT Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GTC GTC tRNAAspGTC Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GCA GCA tRNACysGCA Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TTC TTC tRNAGluTTC Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CTG CTG tRNAGlnCTG Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TTG TTG tRNAGlnTTG Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GCC GCC tRNAGlyGCC Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CCC CCC tRNAGlyCCC Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TCC-1 TCC-1 tRNAGly-1TCC-1 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TCC-2 TCC-2 tRNAGly-2TCC-2 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GTG GTG tRNAHisGTG Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GAT-1 GAT-1 tRNAIleGAT-1 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CAT-1 CAT-1 tRNAile2-1CAT-1 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CAT-2 CAT-2 tRNAile2-1CAT-2 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CAT-3 CAT-3 tRNAile2-3CAT-3 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CAA CAA tRNALeuCAA Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TAA TAA tRNALeuTAA Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TTT-1 TTT-1 tRNALysTTT-1 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TTT-2 TTT-2 tRNALysTTT-2 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CAT CAT tRNAMetCAT Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CAT CAT tRNAfMetCAT Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GAA GAA tRNAPheGAA Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GGA GGA tRNASerGGA Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CGA CGA tRNASerCGA Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TGA TGA tRNASerTGA Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GCT GCT tRNASerGCT Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GGT-1 GGT-1 tRNAThrGGT-1 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GGT-2 GGT-2 tRNAThrGGT-2 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CGT CGT tRNAThrCGT Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TGT-1 TGT-1 tRNAThrTGT-1 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TGT-2 TGT-2 tRNAThrTGT-2 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 CCA CCA tRNATrpCCA Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GTA-1 GTA-1 tRNATyrGTA-1 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GTA-2 GTA-2 tRNATyrGTA-2 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GAC-1 GAC-1 tRNAValGAC-1 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 GAC-2 GAC-2 tRNAValGAC-2 Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TAC TAC tRNAValTAC Anticodon-loop Prokaryotic Cytosol 22378793   
A:t6A RNA tRNA 37 TCA TCA tRNASecTCA Anticodon-loop Prokaryotic Cytosol 22378793   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M R V L G I E T S C D E T G I A I Y D D E K G L L A N Q L Y S Q V K L H A D Y G G V V P E L A S R D H V R K T V P L I Q A A L K E S G L T A K D I D A V A Y T A G P G L V G A L L V G A T V G R S L A F A W D V P A I P V H H M E G H L L A P M L E D N P P E F P F V A L L V S G G H T Q L I S V T G I G Q Y E L L G E S I D D A A G E A F D K T A K L L G L D Y P G G P L L S K M A A Q G T A G R F V F P R P M T D R P G L D F S F S G L K T F A A N T I R D N G T D D Q T R A D I A R A F E D A V V D T L M I K C K R A L D Q T G F K R L V M A G G V S A N R T L R A K L A E M M K K R R G E V F Y A R P E F C T D N G A M I A Y A G M V R F K A G A T A D L G V S V R P R W P L A E L P A 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-P05852-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P05852-F1.cif  
DSSP Secondary Structures   P05852.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D J Biol Chem [details] 22378793 -
A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crecy-Lagard V EMBO J [details] 21285948 -
Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes, which are involved in a universal tRNA modification in Escherichia coli. Hashimoto C, Sakaguchi K, Taniguchi Y, Honda H, Oshima T, Ogasawara N, Kato J J Bacteriol [details] 21873492 -
Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Lauhon CT... Biochemistry [details] 23072323 -