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- PDB-3bju: Crystal Structure of tetrameric form of human lysyl-tRNA synthetase -

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Entry
Database: PDB / ID: 3bju
TitleCrystal Structure of tetrameric form of human lysyl-tRNA synthetase
ComponentsLysyl-tRNA synthetase
KeywordsLIGASE / tRNA synthetase / Lysyl-tRNA / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Phosphoprotein / Polymorphism / Protein biosynthesis
Function / homology
Function and homology information


ATP:ADP adenylyltransferase activity / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / Selenoamino acid metabolism / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex ...ATP:ADP adenylyltransferase activity / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / Selenoamino acid metabolism / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / positive regulation of macrophage activation / tRNA processing / amino acid binding / response to X-ray / ERK1 and ERK2 cascade / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / mitochondrial matrix / positive regulation of DNA-templated transcription / protein homodimerization activity / mitochondrion / extracellular space / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / 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, N-terminal / Lysine-tRNA ligase, class II / 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
ADENOSINE-5'-TRIPHOSPHATE / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsGuo, M. / Yang, X.L. / Schimmel, P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure of tetrameric form of human lysyl-tRNA synthetase: Implications for multisynthetase complex formation
Authors: Guo, M. / Ignatov, M. / Musier-Forsyth, K. / Schimmel, P. / Yang, X.L.
History
DepositionDec 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysyl-tRNA synthetase
B: Lysyl-tRNA synthetase
C: Lysyl-tRNA synthetase
D: Lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,34424
Polymers241,2454
Non-polymers3,09820
Water18,0511002
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lysyl-tRNA synthetase
B: Lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,17212
Polymers120,6232
Non-polymers1,54910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
MethodPISA
3
C: Lysyl-tRNA synthetase
D: Lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,17212
Polymers120,6232
Non-polymers1,54910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.013, 152.013, 108.838
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 60311.301 Da / Num. of mol.: 4 / Fragment: residues 70-579 / Mutation: V582L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KARS, KIAA0070 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon plus / References: UniProt: Q15046, lysine-tRNA ligase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1002 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 277 K / pH: 5.75
Details: 12% PEG8000, 16% Glycerol, 0.08M Na Cacodylate, 0.16M Ca(OAc)2, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2007
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry.
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 160180 / % possible obs: 98 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 0.87 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1E24

1e24


Resolution: 2.31→25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.683 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 5985 5 %RANDOM
Rwork0.194 ---
obs0.197 114762 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0.61 Å20 Å2
2---1.21 Å20 Å2
3---1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.31→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16201 0 176 1002 17379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02216748
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.98322648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93952001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33924.045796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43153038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.45415108
X-RAY DIFFRACTIONr_chiral_restr0.0930.22449
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.38034
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.511248
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.51754
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1670.539
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.373
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.520
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7591.510300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.227216261
X-RAY DIFFRACTIONr_scbond_it1.8337235
X-RAY DIFFRACTIONr_scangle_it2.8644.56382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 438 -
Rwork0.245 8518 -
obs--98.62 %

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