8OU8

Crystal structure of E. coli threonyl tRNA synthetase in complex with a TM84 analogue

PDB DOI: https://doi.org/10.2210/pdb8OU8/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Escherichia coli IAI1
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2023-04-22 Released: 2023-07-12
Deposition Author(s): Rodriguez Buitrago, J.A., Parisini, E., Aigars, J.
Funding Organization(s): European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.266
R-Value Work: 0.189
R-Value Observed: 0.216

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Synthesis and evaluation of an agrocin 84 toxic moiety (TM84) analogue as a malarial threonyl tRNA synthetase inhibitor.

Buitrago, J.A.R., Leitis, G., Kanepe-Lapsa, I., Rudnickiha, A., Parisini, E., Jirgensons, A.

(2023) Org Biomol Chem 21: 5433-5439

PubMed: 37335076 Search on PubMed
DOI: https://doi.org/10.1039/d3ob00670k
Primary Citation of Related Structures:
8OU8

PubMed Abstract:
An analogue of a toxic moiety (TM84) of natural product agrocin 84 containing threonine amide instead of 2,3-dihydroxy-4-methylpentanamide was prepared and evaluated as a putative Plasmodium falciparum threonyl t-RNA synthetase (PfThrRS) inhibitor. This TM84 analogue features submicromolar inhibitory potency (IC ₅₀ = 440 nM) comparable to that of borrelidin (IC ₅₀ = 43 nM) and therefore complements chemotypes known to inhibit malarial PfThrRS, which are currently limited to borrelidin and its analogues. The crystal structure of the inhibitor in complex with the E. coli homologue enzyme (EcThrRS) was obtained, revealing crucial ligand-protein interactions that will pave the way for the design of novel ThrRS inhibitors.

Organizational Affiliation

Latvian Institute of Organic Synthesis, Riga LV-1006, Latvia.

Macromolecule Content

Total Structure Weight: 97.27 kDa
Atom Count: 6,821
Modelled Residue Count: 799
Deposited Residue Count: 822
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonine--tRNA ligase	A [auth D], B [auth A]	411	Escherichia coli IAI1	Mutation(s): 0 Gene Names: thrS, ECIAI1_1775 EC: 6.1.1.3
UniProt
Find proteins for P0A8M3 (Escherichia coli (strain K12)) Explore P0A8M3 Go to UniProtKB: P0A8M3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A8M3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W0U Query on W0U Download Ideal Coordinates CCD File SDF format, chain C [auth D] SDF format, chain G [auth A] MOL2 format, chain C [auth D] MOL2 format, chain G [auth A] mmCIF format, chain C [auth D] mmCIF format, chain G [auth A]	C [auth D], G [auth A]	[(2~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-~{N}-[(2~{S},3~{S})-2-azanyl-3-oxidanyl-butanoyl]phosphonamidic acid C₁₄ H₂₂ N₇ O₇ P ATWLNPAQYPTPKC-UDFANUMJSA-N		Interactions Focus chain C [auth D] Focus chain G [auth A] Interactions & Density Focus chain C [auth D] Focus chain G [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D SDF format, chain H [auth A] MOL2 format, chain D MOL2 format, chain H [auth A] mmCIF format, chain D mmCIF format, chain H [auth A]	D, H [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D Focus chain H [auth A] Interactions & Density Focus chain D Focus chain H [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain J [auth A] MOL2 format, chain E [auth D] MOL2 format, chain J [auth A] mmCIF format, chain E [auth D] mmCIF format, chain J [auth A]	E [auth D], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain J [auth A] Interactions & Density Focus chain E [auth D] Focus chain J [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A]	F [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain I [auth A]