Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA N6-threonylcarbamoyladenosine(37) synthesis protein
Synonym: YeaZ
GI: 16129761
COG: COG1214
UniProt: P76256
Structures: | 1OKJ | 4WQ4 | 4WQ5 | 4YDU | 6Z81 |
Alpha Fold Predicted Structure: AF-P76256-F1
Complex: TsaBDE
Enzyme type: endopeptidase
Position of modification - modification: t:37 - t6A


PDB Structures:


1OKJ

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:

MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLRNNVAWKKLPGKE

Comments:

In bacteria four proteins: TsaC, TsaB, TsaD and TsaE (YrdC, YeaZ, YgjD and YjeE, respectively) are both necessary and sufficient for t6A biosynthesis in vitro. YrdC and YgjD are members of universally conserved families while YeaZ and YjeE are specific to bacteria. TsaB shows homology with YgjD (TsaD) and interacts physically with YjeE (TsaE) and YgjD (TsaD). Together with YjeE, TsaB may also regulate the activity of YgjD.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P76256-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P76256-F1.cif  
DSSP Secondary Structures   P76256.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 -
Conserved network of proteins essential for bacterial viability. Handford JI, Ize B, Buchanan G, Butland GP, Greenblatt J, Emili A, Palmer T J Bacteriol [details] 19376873 -
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 -
Structural analysis of the essential resuscitation promoting factor YeaZ suggests a mechanism of nucleotide regulation through dimer reorganization. Aydin I, Saijo-Hamano Y, Namba K, Thomas C, Roujeinikova A PLoS One [details] 21858042 -
Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Lauhon CT... Biochemistry [details] 23072323 -