4RDH
Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA
Summary for 4RDH
| Entry DOI | 10.2210/pdb4rdh/pdb |
| Related | 4RDI |
| Descriptor | tRNA threonylcarbamoyladenosine dehydratase, ADENOSINE MONOPHOSPHATE, GLYCEROL, ... (5 entities in total) |
| Functional Keywords | rossman fold, dehydratase, ligase |
| Biological source | Escherichia coli |
| Cellular location | Membrane ; Single-pass membrane protein : Q46927 |
| Total number of polymer chains | 4 |
| Total formula weight | 126798.61 |
| Authors | Park, S.Y.,Kim, S.,Lee, H. (deposition date: 2014-09-19, release date: 2015-08-05, Last modification date: 2024-10-16) |
| Primary citation | Kim, S.,Lee, H.,Park, S. 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., 427:3074-3085, 2015 Cited by PubMed Abstract: 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. PubMed: 26101842DOI: 10.1016/j.jmb.2015.06.005 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.1 Å) |
Structure validation
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