The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity

J Mol Biol. 2015 Sep 25;427(19):3074-85. doi: 10.1016/j.jmb.2015.06.005. Epub 2015 Jun 21.


Escherichia coli TcdA (also known as CsdL) was previously shown to catalyze the ATP-dependent dehydration/cyclization of hypermodified tRNA N(6)-threonylcarbamoyladenosine into further cyclic N(6)-threonylcarbamoyladenosine. In this study, we report the X-ray crystal structures of E. coli TcdA with either AMP or ATP bound. The AMP/ATP-bound N-terminal sub-domain of TcdA resembles the ATP-binding Rossmann fold of E. coli ThiF and MoeB that are enzymes respectively taking part in the biosynthesis of thiamine and molybdopterin; however, the remaining C-terminal sub-domain of TcdA adopts a structure unrelated to any other known folds. In TcdA, the ATP-utilizing adenylation of tRNA N(6)-threonylcarbamoyladenosine and a subsequent thioester formation via an active cysteine, similar to the mechanisms in ThiF and MoeB, could take place for the dehydratase function. Analysis of the structure with sequence alignment suggests the disordered Cys234 of TcdA as the most likely catalytic residue. The structure further indicates that the C-terminal sub-domain can provide a binding interface for the tRNA substrate. Binding study using the surface mutants of TcdA and tRNA reveals that the positively charged regions of mainly the C-terminal sub-domain are important for the tRNA recognition.

Keywords: CsdL; N(6)-threonylcarbamoyladenosine dehydratase; RNA modification; TcdA; structural biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / analogs & derivatives*
  • Adenosine / metabolism
  • Adenosine Triphosphate / metabolism
  • Amino Acid Sequence
  • Crystallography, X-Ray
  • Escherichia coli / chemistry
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism*
  • Hydro-Lyases / chemistry
  • Hydro-Lyases / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Multimerization
  • RNA, Transfer / metabolism*
  • Sequence Alignment
  • Ubiquitin-Activating Enzymes / chemistry*
  • Ubiquitin-Activating Enzymes / metabolism*


  • CsdL protein, E coli
  • Escherichia coli Proteins
  • N(6)-(N-threonylcarbonyl)adenosine
  • Adenosine Triphosphate
  • RNA, Transfer
  • Hydro-Lyases
  • Ubiquitin-Activating Enzymes
  • Adenosine

Associated data

  • PDB/4RDH
  • PDB/4RDI
  • PDB/4YED