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- PDB-8xp4: Crystal Structure of human lysyl-tRNA synthetase with acetyllysine -

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Basic information

Entry
Database: PDB / ID: 8xp4
TitleCrystal Structure of human lysyl-tRNA synthetase with acetyllysine
ComponentsLysine--tRNA ligase
KeywordsLIGASE
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 / Selenoamino acid metabolism / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation ...ATP:ADP adenylyltransferase activity / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / Selenoamino acid metabolism / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA processing / amino acid binding / response to X-ray / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / 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 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...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 / 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, OB-fold
Similarity search - Domain/homology
N(6)-ACETYLLYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsZhang, X. / Li, N. / Guo, Y.R. / Ouyang, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of human lysyl-tRNA synthetase with acetyllysine
Authors: Zhang, X. / Li, N. / Guo, Y.R. / Ouyang, Z.
History
DepositionJan 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,7714
Polymers120,3942
Non-polymers3762
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.337, 90.469, 107.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 60197.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KARS1, KARS, KIAA0070 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15046, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, lysine-tRNA ligase
#2: Chemical ChemComp-ALY / N(6)-ACETYLLYSINE


Type: L-peptide linking / Mass: 188.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 289 K / Method: evaporation, recrystallization
Details: 0.06 M Morpheus Divalents, 0.1 M Morpheus Buffer system 1, pH 6.5 and 30% Morpheus Precipitant Mix 2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.26→23.44 Å / Num. obs: 114081 / % possible obs: 99.51 % / Redundancy: 13.4 % / Biso Wilson estimate: 35.66 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2169 / Rpim(I) all: 0.06223 / Rrim(I) all: 0.2258 / Net I/σ(I): 7.77
Reflection shellResolution: 2.26→2.341 Å / Num. unique obs: 5822 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→23.44 Å / SU ML: 0.2558 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.9659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 3804 3.33 %
Rwork0.2388 110276 -
obs0.2397 114080 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.33 Å2
Refinement stepCycle: LAST / Resolution: 2.26→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7944 0 26 192 8162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328163
X-RAY DIFFRACTIONf_angle_d0.575511018
X-RAY DIFFRACTIONf_chiral_restr0.04211197
X-RAY DIFFRACTIONf_plane_restr0.00631426
X-RAY DIFFRACTIONf_dihedral_angle_d14.43313123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.290.26821280.34823762X-RAY DIFFRACTION93
2.29-2.320.32871390.32614139X-RAY DIFFRACTION99.95
2.32-2.350.33911400.31414070X-RAY DIFFRACTION99.86
2.35-2.380.33391430.30644125X-RAY DIFFRACTION99.72
2.38-2.420.34331410.30774104X-RAY DIFFRACTION99.84
2.42-2.460.35891420.2964081X-RAY DIFFRACTION99.72
2.46-2.50.30021420.29974061X-RAY DIFFRACTION99.46
2.5-2.540.34091430.28514071X-RAY DIFFRACTION99.81
2.54-2.590.25961420.28454139X-RAY DIFFRACTION99.81
2.59-2.640.25181390.27414079X-RAY DIFFRACTION99.74
2.64-2.690.31430.26964121X-RAY DIFFRACTION99.79
2.69-2.750.3351360.27314082X-RAY DIFFRACTION99.32
2.75-2.810.37161400.26534112X-RAY DIFFRACTION99.79
2.81-2.880.31071420.26394054X-RAY DIFFRACTION99.69
2.88-2.960.23991440.25614119X-RAY DIFFRACTION99.86
2.96-3.050.22391400.25154096X-RAY DIFFRACTION99.79
3.05-3.140.2341420.24784095X-RAY DIFFRACTION99.98
3.14-3.260.31141420.2544119X-RAY DIFFRACTION99.93
3.26-3.390.25031380.23934081X-RAY DIFFRACTION99.79
3.39-3.540.24521420.23824072X-RAY DIFFRACTION99.79
3.54-3.730.2551430.22314127X-RAY DIFFRACTION99.91
3.73-3.960.28391400.21194101X-RAY DIFFRACTION99.84
3.96-4.260.25741450.21024090X-RAY DIFFRACTION99.88
4.26-4.690.23611410.17684121X-RAY DIFFRACTION99.95
4.69-5.360.22941410.19484082X-RAY DIFFRACTION99.81
5.36-6.730.24041440.23534104X-RAY DIFFRACTION99.86
6.73-23.440.19831420.21714069X-RAY DIFFRACTION99.08
Refinement TLS params.Method: refined / Origin x: 13.6177271382 Å / Origin y: -0.0254466696877 Å / Origin z: 0.313294886677 Å
111213212223313233
T0.272544636625 Å20.00122688689346 Å20.00317726627225 Å2-0.270409619031 Å2-0.0103589087493 Å2--0.372024973825 Å2
L0.178522748483 °2-0.211117515761 °20.037882449331 °2-0.36982298511 °2-0.0113486128154 °2--0.0715156735857 °2
S0.0437753169179 Å °0.0164857909725 Å °-0.0335236698628 Å °0.0270627534076 Å °-0.0787104633064 Å °0.0483302993457 Å °-0.0151386480415 Å °0.00607307611247 Å °-9.75044925334E-5 Å °
Refinement TLS groupSelection details: all

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