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- PDB-6ilh: Crystal Structure of human lysyl-tRNA synthetase L350H mutant -

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Basic information

Entry
Database: PDB / ID: 6ilh
TitleCrystal Structure of human lysyl-tRNA synthetase L350H mutant
ComponentsLysine-tRNA ligase
KeywordsLIGASE / lysyl-tRNA synthetase / LysRS / disease related mutant
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 / 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
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsHei, Z. / Liu, Z. / Wang, J. / Fang, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21778064 China
National Natural Science Foundation of China21778067 China
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex.
Authors: Hei, Z. / Wu, S. / Liu, Z. / Wang, J. / Fang, P.
History
DepositionOct 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,6224
Polymers120,6732
Non-polymers9492
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-41 kcal/mol
Surface area40020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.180, 152.180, 106.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 72 through 74 or (resid 75...
21(chain B and (resid 72 through 215 or resid 219...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASNASN(chain A and (resid 72 through 74 or (resid 75...AA72 - 744 - 6
12GLNGLNGLNGLN(chain A and (resid 72 through 74 or (resid 75...AA757
13VALVALPROPRO(chain A and (resid 72 through 74 or (resid 75...AA71 - 5753 - 507
14VALVALPROPRO(chain A and (resid 72 through 74 or (resid 75...AA71 - 5753 - 507
15VALVALPROPRO(chain A and (resid 72 through 74 or (resid 75...AA71 - 5753 - 507
16VALVALPROPRO(chain A and (resid 72 through 74 or (resid 75...AA71 - 5753 - 507
21ASPASPHISHIS(chain B and (resid 72 through 215 or resid 219...BB72 - 2154 - 147
22GLYGLYMETMET(chain B and (resid 72 through 215 or resid 219...BB219 - 357151 - 289
23GLYGLYGLYGLY(chain B and (resid 72 through 215 or resid 219...BB360 - 380292 - 312
24GLNGLNALAALA(chain B and (resid 72 through 215 or resid 219...BB381 - 382313 - 314
25ASPASPPROPRO(chain B and (resid 72 through 215 or resid 219...BB72 - 5754 - 507
26ASPASPPROPRO(chain B and (resid 72 through 215 or resid 219...BB72 - 5754 - 507
27ASPASPPROPRO(chain B and (resid 72 through 215 or resid 219...BB72 - 5754 - 507
28ASPASPPROPRO(chain B and (resid 72 through 215 or resid 219...BB72 - 5754 - 507

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Components

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


Mass: 60336.293 Da / Num. of mol.: 2 / Mutation: L350H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KARS, KIAA0070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15046, lysine-tRNA ligase
#2: Chemical ChemComp-KAA / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / 5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE


Mass: 474.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N8O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 13% PEG 2000 MME, 0.4M Ammonium acetate pH8.0 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→106.32 Å / Num. obs: 44348 / % possible obs: 89.8 % / Redundancy: 19.1 % / Biso Wilson estimate: 53.85 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.038 / Rrim(I) all: 0.165 / Net I/σ(I): 14.5 / Num. measured all: 844999 / Scaling rejects: 1949
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.5718.70.68435950.9120.1610.70399.5
11.18-106.3217.70.0876260.9970.0210.08999.9

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BJU

3bju


Resolution: 2.501→82.75 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 24.42
RfactorNum. reflection% reflection
Rfree0.226 4257 5.01 %
Rwork0.1938 --
obs0.1954 44302 89.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.08 Å2 / Biso mean: 56.8576 Å2 / Biso min: 29.2 Å2
Refinement stepCycle: final / Resolution: 2.501→82.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7968 0 64 53 8085
Biso mean--47.73 50.29 -
Num. residues----1006
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3024X-RAY DIFFRACTION7.683TORSIONAL
12B3024X-RAY DIFFRACTION7.683TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5009-2.59020.30264810.26519008948999
2.5902-2.6940.34112410.26964186442747
2.694-2.81660.3014070.25558838924597
2.8166-2.96510.28275070.249489579464100
2.9651-3.15090.27334910.241890589549100
3.1509-3.39410.28615360.231189359471100
3.3941-3.73570.2553310.21765638596963
3.7357-4.27620.19843550.17277902825787
4.2762-5.38750.18494100.151391019511100
5.3875-82.7950.17264980.165490279525100
Refinement TLS params.Method: refined / Origin x: -56.6449 Å / Origin y: -3.5118 Å / Origin z: -6.2177 Å
111213212223313233
T0.3267 Å20.0042 Å2-0.0048 Å2-0.4234 Å2-0.0322 Å2--0.3174 Å2
L0.1446 °2-0.074 °2-0.0098 °2-0.4963 °2-0.0026 °2--0.518 °2
S-0.017 Å °0.0006 Å °-0.0121 Å °-0.0169 Å °0.0435 Å °-0.0764 Å °0.0411 Å °0.1453 Å °-0.0173 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA71 - 575
2X-RAY DIFFRACTION1allB72 - 575
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 63

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