6P24 | pdb_00006p24

Escherichia coli tRNA synthetase

PDB DOI: https://doi.org/10.2210/pdb6P24/pdb

Classification: LIGASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-05-20 Released: 2020-11-18
Deposition Author(s): Kahne, D., Baidin, V., Owens, T.W.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.265 (Depositor), 0.270 (DCC)
R-Value Work:
0.229 (Depositor), 0.235 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Simple Secondary Amines Inhibit Growth of Gram-Negative Bacteria through Highly Selective Binding to Phenylalanyl-tRNA Synthetase.

Baidin, V., Owens, T.W., Lazarus, M.B., Kahne, D.

(2021) J Am Chem Soc 143: 623-627

PubMed: 33411531 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacs.0c11113
Primary Citation Related Structures:
6OZ5, 6P24, 6P26, 6P8T

PubMed Abstract:
Antibiotics to treat drug-resistant Gram-negative infections are urgently needed but challenging to discover. Using a cell-based screen, we identified a simple secondary amine that inhibited the growth of wild-type Escherichia coli and Acinetobacter baumannii but not the growth of the Gram-positive organism Bacillus subtilis . Resistance mutations in E. coli and A. baumannii mapped exclusively to the aminoacyl-tRNA synthetase PheRS. We confirmed biochemically that the compound inhibited PheRS from these organisms and showed that it did not inhibit PheRS from B. subtilis or humans. To understand the basis for the compound's high selectivity for only some PheRS enzymes, we solved crystal structures of E. coli and A. baumannii PheRS complexed with the inhibitor. The structures showed that the compound's benzyl group mimics the benzyl of phenylalanine. The other amine substituent, a 2-(cyclohexen-1-yl)ethyl group, induces a hydrophobic pocket in which it binds. Through bioinformatic analysis and mutagenesis, we show that the ability to induce a complementary hydrophobic pocket that can accommodate the second substituent explains the high selectivity of this remarkably simple molecular scaffold for Gram-negative PheRS. Because this secondary amine scaffold is active against wild-type Gram-negative pathogens but is not cytotoxic to mammalian cells, we suggest that it may be possible to develop it for use in combination antibiotic therapy to treat Gram-negative infections.

Organizational Affiliation

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.

Macromolecule Content

Total Structure Weight: 253.45 kDa
Atom Count: 17,272
Modeled Residue Count: 2,151
Deposited Residue Count: 2,254
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanine--tRNA ligase alpha subunit	A, C	332	Escherichia coli K-12	Mutation(s): 0 Gene Names: pheS, b1714, JW5277 EC: 6.1.1.20
UniProt
Find proteins for P08312 (Escherichia coli (strain K12)) Explore P08312 Go to UniProtKB: P08312
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08312
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanine--tRNA ligase beta subunit	B, D	795	Escherichia coli K-12	Mutation(s): 0 Gene Names: pheT, b1713, JW1703 EC: 6.1.1.20
UniProt
Find proteins for P07395 (Escherichia coli (strain K12)) Explore P07395 Go to UniProtKB: P07395
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07395
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain BA [auth B] MOL2 format, chain U [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain U [auth B] mmCIF format, chain BA [auth B]	BA [auth B], U [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain U [auth B] Interactions & Density Focus chain BA [auth B] Focus chain U [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain SA [auth D] SDF format, chain O [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] mmCIF format, chain SA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C]	KA [auth C], L [auth A], O [auth A], SA [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain KA [auth C] Focus chain L [auth A] Focus chain O [auth A] Focus chain SA [auth D] Interactions & Density Focus chain KA [auth C] Focus chain L [auth A] Focus chain O [auth A] Focus chain SA [auth D]
HEZ Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain PA [auth D] SDF format, chain OA [auth D] SDF format, chain K [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain K [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain K [auth A]	K [auth A], OA [auth D], PA [auth D], QA [auth D], RA [auth D]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Interactions & Density Focus chain K [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain YA [auth D] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain T [auth B] SDF format, chain M [auth A] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain AB [auth D] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain T [auth B] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain AB [auth D] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain T [auth B] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain AB [auth D] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth D] HA [auth C] IA [auth C] M [auth A] AA [auth B], AB [auth D], HA [auth C], IA [auth C], M [auth A], T [auth B], X [auth B], Y [auth B], YA [auth D], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain M [auth A] Focus chain T [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain M [auth A] Focus chain T [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain ZA [auth D] SDF format, chain XA [auth D] SDF format, chain WA [auth D] SDF format, chain W [auth B] SDF format, chain VA [auth D] SDF format, chain V [auth B] SDF format, chain UA [auth D] SDF format, chain TA [auth D] SDF format, chain N [auth A] SDF format, chain LA [auth C] SDF format, chain JA [auth C] SDF format, chain GA [auth C] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BB [auth D] MOL2 format, chain ZA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth D] mmCIF format, chain ZA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth D]	BB [auth D] CA [auth B] CB [auth D] DA [auth B] DB [auth D] BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], GA [auth C], JA [auth C], LA [auth C], N [auth A], TA [auth D], UA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], XA [auth D], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain GA [auth C] Focus chain JA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain GA [auth C] Focus chain JA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain ZA [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain NA [auth D] SDF format, chain MA [auth D] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth C] SDF format, chain F [auth A] SDF format, chain EA [auth C] SDF format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain E [auth A]	E [auth A] EA [auth C] F [auth A] FA [auth C] G [auth A] E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], H [auth A], I [auth A], MA [auth D], NA [auth D], P [auth B], Q [auth B], R [auth B], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.265 (Depositor), 0.270 (DCC)
R-Value Work: 0.229 (Depositor), 0.235 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.269	α = 90
b = 173.583	β = 90
c = 251.472	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Kahne, D.

Baidin, V.

Owens, T.W.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19-AI109764-05-8340

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2021-01-20
Changes: Database references
Version 1.2: 2021-02-03
Changes: Database references
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description