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- PDB-9tjv: Ternary complex of E. coli leucyl-tRNA synthetase mutant W177A, t... -

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Basic information

Entry
Database: PDB / ID: 9tjv
TitleTernary complex of E. coli leucyl-tRNA synthetase mutant W177A, tRNA(leu) and the leucyl adenylate analog LeuAMS in the aminoacyl transfer state
Components
  • Leucine--tRNA ligase
  • tRNA(leu)
KeywordsRNA BINDING PROTEIN / Leucine tRNA ligase Antimicrobial target tRNA aminoacylation for protein translation
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
5'-O-(L-leucylsulfamoyl)adenosine / : / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.277 Å
AuthorsHoffmann, G. / Palencia, A.
Funding support France, European Union, 4items
OrganizationGrant numberCountry
Grenoble Instruct-ERIC Center (ISBG)27604 France
iNEXT-Discovery45625European Union
Agence Nationale de la Recherche (ANR)ANR-20-AMRB-0003 France
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0040 France
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: The Zn Domain Acts as a Dynamic Switch Coordinating Multiple-Step Aminoacylation in Bacterial Leucyl-tRNA Synthetase
Authors: Hoffmann, G. / Dulic, M. / Gruic-Sovulj, I. / Palencia, A.
History
DepositionDec 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 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)
C: Leucine--tRNA ligase
D: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,8758
Polymers254,9074
Non-polymers9684
Water12,520695
1
A: Leucine--tRNA ligase
B: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9625
Polymers127,4542
Non-polymers5083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-63 kcal/mol
Surface area46060 Å2
MethodPISA
2
C: Leucine--tRNA ligase
D: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9133
Polymers127,4542
Non-polymers4591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-42 kcal/mol
Surface area46690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.009, 68.312, 226.276
Angle α, β, γ (deg.)90, 104.44, 90
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 99400.883 Da / Num. of mol.: 2 / Mutation: W177A
Source method: isolated from a genetically manipulated source
Details: E. coli Leucyl tRNA synthetase with W177A mutation / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: leuS, BWG_0513 / Production host: Escherichia coli (E. coli) / References: UniProt: C4ZWC9, leucine-tRNA ligase
#2: RNA chain tRNA(leu)


Mass: 28052.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: E. coli tRNA(Leu) isoacceptor UAA / Source: (gene. exp.) Escherichia coli (E. coli)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 1231762938
#3: Chemical ChemComp-LSS / 5'-O-(L-leucylsulfamoyl)adenosine / 5-O-N-LEUCYL-SULFAMOYLADENOSINE


Mass: 459.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M BisTris pH5.5, 0.2M Ammonium Acetate, 23-26% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.28→219.132 Å / Num. obs: 84189 / % possible obs: 92 % / Redundancy: 3.3 % / Biso Wilson estimate: 40.1 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.083 / Rrim(I) all: 0.152 / Net I/σ(I): 5.2
Reflection shellResolution: 2.28→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4209 / CC1/2: 0.591 / Rpim(I) all: 0.486 / Rrim(I) all: 0.915 / % possible all: 43.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC20240123data reduction
STARANISOdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.277→219.13 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.537 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.574 / SU Rfree Blow DPI: 0.249 / SU Rfree Cruickshank DPI: 0.249
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 4265 -RANDOM
Rwork0.1938 79924 --
obs0.1953 84189 78.3 %-
Displacement parametersBiso mean: 67.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.5856 Å2
2---1.5616 Å20 Å2
3---1.2517 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: LAST / Resolution: 2.277→219.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13534 3307 64 695 17600
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00717607HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8124649HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5572SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2529HARMONIC5
X-RAY DIFFRACTIONt_it17607HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2393SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12258SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion16.85
LS refinement shellResolution: 2.28→2.43 Å
RfactorNum. reflection% reflection
Rfree0.2928 88 -
Rwork0.2546 1596 -
obs0.2566 1684 9 %
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)
11.24310.2550.45781.08490.05610.2374-0.1177-0.15790.14260.12290.06230.2551-0.0274-0.05530.0554-0.08130.00040.0769-0.03960.00720.0432-57.83879.1478-85.2114
20.20030.04840.04190.3874-0.19870.09510.0112-0.05820.01720.057-0.01040.0103-0.01480.0036-0.0008-0.0165-0.01210.0317-0.0689-0.01250.0288-31.70398.9699-84.116
33.93190.4503-0.54320.4888-0.82740.7826-0.002-0.8143-0.5677-0.292-0.0359-0.0890.4202-0.05440.03790.24190.0842-0.03310.09520.2775-0.4606-69.603313.487-27.515
41.04410.64070.40290.4035-0.66531.11230.1429-0.27450.0991-0.0692-0.14690.010.13230.08220.0040.08860.1785-0.00460.13180.0354-0.4121-52.22732.1998-29.2948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B1 - 76
2X-RAY DIFFRACTION2{ A|* }A0 - 860
3X-RAY DIFFRACTION2{ A|* }A901
4X-RAY DIFFRACTION3{ D|* }D1 - 76
5X-RAY DIFFRACTION4{ C|* }C1 - 860
6X-RAY DIFFRACTION4{ C|* }C901

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