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- PDB-9twt: Complex of E. coli leucyl-tRNA synthetase AN3365-resistant mutant... -

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Basic information

Entry
Database: PDB / ID: 9twt
TitleComplex of E. coli leucyl-tRNA synthetase AN3365-resistant mutant D251N bound to tRNA(leu) and AN3365
Components
  • Leucine--tRNA ligase
  • tRNA(leu)
KeywordsRNA BINDING PROTEIN / Leucine tRNA ligase Antimicrobial target resistant mutant Epetraborole
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-365 / : / : / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsHoffmann, G. / Palencia, A. / Muller, B.
Funding supportEuropean Union, France, 4items
OrganizationGrant numberCountry
iNEXT-Discovery45625European Union
Grenoble Instruct-ERIC Center (ISBG)27604 France
Agence Nationale de la Recherche (ANR)ANR-20-AMRB-0003 France
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0040 France
CitationJournal: Nat Commun / Year: 2026
Title: Mechanisms of Resistance to an Antibiotic Targeting Bacterial Leucyl-tRNA Synthetase
Authors: Muller, B. / Fries, F. / Huber, A.L. / Risch, T. / Mohamadyar-Toupkanlou, F. / Hoffmann, G. / Dulic, M. / Herrmann, J. / Guic Sovulj, I. / Muller, R. / Palencia, A.
History
DepositionJan 15, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine--tRNA ligase
B: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0914
Polymers127,2382
Non-polymers8532
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-38 kcal/mol
Surface area45870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.581, 72.323, 104.87
Angle α, β, γ (deg.)90, 115.3, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 99515.031 Da / Num. of mol.: 1 / Mutation: D251N
Source method: isolated from a genetically manipulated source
Details: E. coli Leucyl tRNA synthetase D251N mutant / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: leuS, b0642, JW0637 / Production host: Escherichia coli (E. coli) / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain tRNA(leu)


Mass: 27723.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: E. coli tRNA(Leu) isoacceptor UAA with A76 forming an adduct with AN3665
Source: (gene. exp.) Escherichia coli (E. coli)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 1845258627
#3: Chemical ChemComp-A1JX6 / (2~{S})-2-azanyl-~{N}-[azanyl-(3-fluorophenyl)-oxidanylidene-$l^{6}-sulfanylidene]-4-methyl-pentanamide


Mass: 287.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18FN3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-365 / [(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl dihydrogen phosphate / 3-AMINOMETHYL-7-(3-HYDROXY-PROPOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine


Mass: 565.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27BN6O10P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M KH2PO4, 19-23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 12, 2022 / Details: Vertical CRL / Horizontal CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.3→83.22 Å / Num. obs: 40504 / % possible obs: 93.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.049 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.55 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2026 / CC1/2: 0.545 / Rpim(I) all: 0.522 / % possible all: 60.5

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.299→83.22 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.562 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.59 / SU Rfree Blow DPI: 0.297 / SU Rfree Cruickshank DPI: 0.298
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1979 -RANDOM
Rwork0.2005 38525 --
obs0.2032 40504 71.5 %-
Displacement parametersBiso mean: 60.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.405 Å20 Å2-1.1344 Å2
2--1.3337 Å20 Å2
3----1.7388 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å
Refinement stepCycle: LAST / Resolution: 2.299→83.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6265 1775 57 293 8390
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078459HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8311882HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2646SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1191HARMONIC5
X-RAY DIFFRACTIONt_it8459HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1153SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5906SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion18.28
LS refinement shellResolution: 2.3→2.46 Å
RfactorNum. reflection% reflection
Rfree0.3114 40 -
Rwork0.2696 771 -
obs0.2717 811 7.77 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8159-1.705-0.75692.17120.5334-0.3534-0.05910.37630.3409-0.17710.1069-0.0333-0.1680.1538-0.0478-0.17290.0534-0.03540.236-0.0214-0.174728.97959.099123.7063
20.53480.1450.01190.22420.15080.51310.04460.0987-0.0610.0924-0.02450.07830.02870.116-0.02010.00340.0263-0.0282-0.04230.0041-0.06213.3044-2.881622.942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B1 - 75
2X-RAY DIFFRACTION1{ B|* }B76
3X-RAY DIFFRACTION2{ A|* }A1 - 859
4X-RAY DIFFRACTION2{ A|* }A901

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