6S84 | pdb_00006s84

TsaBDE complex from Thermotoga maritima

PDB DOI: https://doi.org/10.2210/pdb6S84/pdb
Entry: 6S84 supersedes: 6FPE

Classification: RNA BINDING PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-08 Released: 2019-07-17
Deposition Author(s): Missoury, S., Li-de-La-Sierra-Gallay, I., van Tilbeurgh, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.282 (Depositor), 0.271 (DCC)
R-Value Work:
0.209 (Depositor), 0.199 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

PubMed: 29741707 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gky323
Primary Citation 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. 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.

Macromolecule Content

Total Structure Weight: 162.61 kDa
Atom Count: 10,687
Modeled Residue Count: 1,341
Deposited Residue Count: 1,434
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA N6-adenosine threonylcarbamoyltransferase	A, C [auth D]	327	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: tsaD, gcp, TM_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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WXZ2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase YjeE, predicted to have essential role in cell wall biosynthesis	B [auth E], F [auth B]	184	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: Tmari_1641

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB	D [auth C], E [auth F]	206	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: tsaB, TM_0874, Tmari_0876
UniProt
Find proteins for Q9WZX7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZX7 Go to UniProtKB: Q9WZX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WZX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APC Query on APC Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain J [auth D] SDF format, chain I [auth E] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain J [auth D] MOL2 format, chain I [auth E] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain J [auth D] mmCIF format, chain I [auth E] mmCIF format, chain G [auth A]	G [auth A], I [auth E], J [auth D], M [auth B]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ CAWZRIXWFRFUQB-IOSLPCCCSA-N		Interactions Focus chain G [auth A] Focus chain I [auth E] Focus chain J [auth D] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth E] Focus chain J [auth D] Focus chain M [auth B]
LEU Query on LEU Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	LEUCINE C₆ H₁₃ N O₂ ROHFNLRQFUQHCH-YFKPBYRVSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth E] MOL2 format, chain L [auth B] MOL2 format, chain H [auth E] mmCIF format, chain L [auth B] mmCIF format, chain H [auth E]	H [auth E], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth E] Focus chain L [auth B] Interactions & Density Focus chain H [auth E] Focus chain L [auth B]