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- PDB-6l3y: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falcip... -

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Basic information

Entry
Database: PDB / ID: 6l3y
TitleCrystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-C
ComponentsLysine--tRNA ligase
KeywordsPROTEIN BINDING/INHIBITOR / Inhibitor / Cladosporin analog / Stereochemistry / PROTEIN BINDING / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


Transcriptional and post-translational regulation of MITF-M expression and activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-E5C / LYSINE / PHOSPHATE ION / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBabbar, P. / Sharma, A. / Mishra, S. / Manickam, Y. / Harlos, K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR13636 India
Citation
Journal: Chembiochem / Year: 2021
Title: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin inhibitor, Cla-B
Authors: Babbar, P. / Sato, M. / Manickam, Y. / Mishra, S. / Harlos, K. / Gupta, S. / Parvez, S. / Kikuchi, H. / Sharma, A.
#1: Journal: J. Struct. Funct. Genomics / Year: 2014
Title: Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin.
Authors: Khan, S. / Sharma, A. / Belrhali, H. / Yogavel, M. / Sharma, A.
History
DepositionOct 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Lysine--tRNA ligase
A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,79411
Polymers117,4142
Non-polymers1,3809
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-45 kcal/mol
Surface area40630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)299.841, 52.831, 70.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase


Mass: 58706.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1350100 / Plasmid: petm41 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IDJ8, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-E5C / (3R)-3-[[(3S)-3-ethylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one


Mass: 305.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.13 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.09M NPS-0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic,0.3M Ammonium sulfate. 1.0M Buffer-pH6.5- Imidazole; MES monohydrate (acid) Precipitant Mix-25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.89→149.921 Å / Num. obs: 25891 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.989 / Net I/σ(I): 5.7
Reflection shellResolution: 2.898→2.948 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1293 / CC1/2: 0.446 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PG3

4pg3


Resolution: 3.1→74.96 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 1059 5 %
Rwork0.2252 20140 -
obs0.228 21199 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.58 Å2 / Biso mean: 57.6733 Å2 / Biso min: 26.95 Å2
Refinement stepCycle: final / Resolution: 3.1→74.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7899 0 89 20 8008
Biso mean--57.94 45.3 -
Num. residues----966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.1-3.24110.31151120.29252447
3.2411-3.4120.35961370.26472469
3.412-3.62580.32091340.2622453
3.6258-3.90570.32021410.22782489
3.9057-4.29870.26381490.2062471
4.2987-4.92070.23721260.18512531
4.9207-6.19910.28081390.21332546
6.1991-74.960.24441210.22242734

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