9DRS | pdb_00009drs

Crystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-116

PDB DOI: https://doi.org/10.2210/pdb9DRS/pdb
NAKB: 9DRS

Classification: LIGASE/RNA
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-26 Released: 2025-02-12
Deposition Author(s): Gade, P., Chang, C., Forte, B., Wower, J., Gilbert, I.H., Baragana, B., Michalska, K., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Different chemical scaffolds bind to L-phe site in Mycobacterium tuberculosis Phe-tRNA synthetase.

Gade, P., Chang, C., Pryde, D.S., Fletcher, D., Niven, S., Magalhaes, L.G., Robinson, D., Saini, J., Ibrahim, P.E.G.F., Forte, B., Wower, J., Bodkin, M.J., Baragana, B., Gilbert, I.H., Michalska, K., Joachimiak, A.

(2025) Eur J Med Chem 287: 117335-117335

PubMed: 39919438 Search on PubMed
DOI: https://doi.org/10.1016/j.ejmech.2025.117335
Primary Citation Related Structures:
9DRS, 9DRT, 9DRV, 9DSX, 9DTF

PubMed Abstract:
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mt), is one of the deadliest infectious diseases. The rise of multidrug-resistant strains represents a major public health threat, requiring new therapeutic options. Bacterial aminoacyl-tRNA synthetases (aaRS) have been shown to be highly promising drug targets, including for TB treatment. These enzymes play an essential role in translating the DNA gene code into protein sequence by attaching specific amino acid to their cognate tRNAs. They have multiple binding sites that can be targeted for inhibitor discovery: amino acid binding pocket, ATP binding pocket, tRNA binding site and an editing domain. Recently we reported several high-resolution structures of M. tuberculosis phenylalanyl-tRNA synthetase (MtPheRS) complexed with tRNA ^Phe and either L-Phe or a nonhydrolyzable phenylalanine adenylate analog. Here, using Nucleic Magnetic Resonance (NMR) and Surface Plasmon Resonance (SPR) we identified fragments that bind to MtPheRS and we determined crystal structures of their complexes with MtPheRS/tRNA ^Phe. All the binders interact with the L-Phe amino acid binding site. The analysis of interactions of the new compounds combined with adenylate analog structure provides insights for the rational design of anti-tuberculosis drugs. The 3' arm of the tRNA ^Phe in all the structures was disordered with exception of one complex with D-735 compound. In this structure the 3' CCA end of the acceptor stem is observed in the editing domain of MtPheRS providing insights regarding the post-transfer editing activity of class II aaRS.

Organizational Affiliation

Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA; Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA.

Macromolecule Content

Total Structure Weight: 304.87 kDa
Atom Count: 21,276
Modeled Residue Count: 2,451
Deposited Residue Count: 2,506
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanine--tRNA ligase alpha subunit	A, D	341	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pheS, Rv1649, MTCY06H11.14 EC: 6.1.1.20
UniProt
Find proteins for P9WFU3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFU3 Go to UniProtKB: P9WFU3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WFU3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanine--tRNA ligase beta subunit	B, E	835	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pheT, Rv1650, MTCY06H11.15 EC: 6.1.1.20
UniProt
Find proteins for P9WFU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFU1 Go to UniProtKB: P9WFU1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WFU1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
tRNA(Phe)	C, F	77	Mycobacterium tuberculosis H37Rv
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
AX7 (Subject of Investigation/LOI) Query on AX7 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D]	G [auth A], GA [auth D]	1H-benzimidazol-2-amine C₇ H₇ N₃ JWYUFVNJZUSCSM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain GA [auth D] Interactions & Density Focus chain G [auth A] Focus chain GA [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain LA [auth E] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Z [auth B] MOL2 format, chain LA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain LA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth B]	LA [auth E], O [auth B], P [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain LA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain Z [auth B] Interactions & Density Focus chain LA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain Z [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain JA [auth D] MOL2 format, chain JA [auth D] mmCIF format, chain JA [auth D]	JA [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Interactions & Density Focus chain JA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain KA [auth E] SDF format, chain L [auth B] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	AA [auth C] KA [auth E] L [auth B] PA [auth E] QA [auth E] AA [auth C], KA [auth E], L [auth B], PA [auth E], QA [auth E], RA [auth E], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain KA [auth E] Focus chain L [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain AA [auth C] Focus chain KA [auth E] Focus chain L [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain W [auth B] Focus chain X [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain MA [auth E] SDF format, chain N [auth B] SDF format, chain OA [auth E] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain NA [auth E] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain OA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain NA [auth E] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth E] mmCIF format, chain N [auth B] mmCIF format, chain OA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain NA [auth E] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	BA [auth C] I [auth A] IA [auth D] J [auth A] K [auth B] BA [auth C], I [auth A], IA [auth D], J [auth A], K [auth B], M [auth B], MA [auth E], N [auth B], NA [auth E], OA [auth E], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain MA [auth E] Focus chain N [auth B] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain BA [auth C] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain MA [auth E] Focus chain N [auth B] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain SA [auth F] SDF format, chain EA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain SA [auth F] MOL2 format, chain EA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain SA [auth F] mmCIF format, chain EA [auth C]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] H [auth A] CA [auth C], DA [auth C], EA [auth C], FA [auth C], H [auth A], HA [auth D], SA [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain H [auth A] Focus chain HA [auth D] Focus chain SA [auth F] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain H [auth A] Focus chain HA [auth D] Focus chain SA [auth F]