6S84 image
Deposition Date 2019-07-08
Release Date 2019-07-17
Last Version Date 2024-05-15
Entry Detail
PDB ID:
6S84
Title:
TsaBDE complex from Thermotoga maritima
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.89 Å
R-Value Free:
0.28
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:tRNA N6-adenosine threonylcarbamoyltransferase
Gene (Uniprot):tsaD
Chain IDs:A, C (auth: D)
Chain Length:327
Number of Molecules:2
Biological Source:Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Gene (Uniprot):tsaB
Chain IDs:D (auth: C), E (auth: F)
Chain Length:206
Number of Molecules:2
Biological Source:Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Polymer Type:polypeptide(L)
Molecule:ATPase YjeE, predicted to have essential role in cell wall biosynthesis
Chain IDs:B (auth: E), F (auth: B)
Chain Length:184
Number of Molecules:2
Biological Source:Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Primary Citation
The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification.
Nucleic Acids Res. 46 5850 5860 (2018)
PMID: 29741707 DOI: 10.1093/nar/gky323

Abstact

The universal N6-threonylcarbamoyladenosine (t6A) modification at position A37 of ANN-decoding tRNAs is essential for translational fidelity. In bacteria the TsaC enzyme first synthesizes an l-threonylcarbamoyladenylate (TC-AMP) intermediate. In cooperation with TsaB and TsaE, TsaD then transfers the l-threonylcarbamoyl-moiety from TC-AMP onto tRNA. We determined the crystal structure of the TsaB-TsaE-TsaD (TsaBDE) complex of Thermotoga maritima in presence of a non-hydrolysable AMPCPP. TsaE is positioned at the entrance of the active site pocket of TsaD, contacting both the TsaB and TsaD subunits and prohibiting simultaneous tRNA binding. AMPCPP occupies the ATP binding site of TsaE and is sandwiched between TsaE and TsaD. Unexpectedly, the binding of TsaE partially denatures the active site of TsaD causing loss of its essential metal binding sites. TsaE interferes in a pre- or post-catalytic step and its binding to TsaBD is regulated by ATP hydrolysis. This novel binding mode and activation mechanism of TsaE offers good opportunities for antimicrobial drug development.

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