6S84

TsaBDE complex from Thermotoga maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification.

Missoury, S.Plancqueel, S.Li de la Sierra-Gallay, I.Zhang, W.Liger, D.Durand, D.Dammak, R.Collinet, B.van Tilbeurgh, H.

(2018) Nucleic Acids Res 46: 5850-5860

  • DOI: 10.1093/nar/gky323
  • Primary Citation of Related Structures:  
    6S84

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA N6-adenosine threonylcarbamoyltransferaseA, C [auth D]327Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: tsaDgcpTM_0145
EC: 2.3.1.234
UniProt
Find proteins for Q9WXZ2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WXZ2 
Go to UniProtKB:  Q9WXZ2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase YjeE, predicted to have essential role in cell wall biosynthesisF [auth B], B [auth E]184Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: Tmari_1641
UniProt
Find proteins for R4NRX5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore R4NRX5 
Go to UniProtKB:  R4NRX5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA threonylcarbamoyladenosine biosynthesis protein TsaBD [auth C], E [auth F]206Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: tsaBTM_0874Tmari_0876
UniProt
Find proteins for Q9WZX7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZX7 
Go to UniProtKB:  Q9WZX7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download Ideal Coordinates CCD File 
G [auth A], I [auth E], J [auth D], M [auth B]DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
LEU
Query on LEU

Download Ideal Coordinates CCD File 
K [auth B]LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth E], L [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.16α = 90
b = 108.21β = 90
c = 176.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release