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- PDB-7ea9: Crystal Structure of human lysyl-tRNA synthetase Y145H mutant -

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Basic information

Entry
Database: PDB / ID: 7ea9
TitleCrystal Structure of human lysyl-tRNA synthetase Y145H 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 / 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 / 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, 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 / 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
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWu, S. / Hei, Z. / Zheng, L. / Zhou, J. / Liu, Z. / Wang, J. / Fang, P.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778064 China
National Natural Science Foundation of China (NSFC)21778067 China
National Natural Science Foundation of China (NSFC)21977107 China
National Natural Science Foundation of China (NSFC)21977108 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural analyses of a human lysyl-tRNA synthetase mutant associated with autosomal recessive nonsyndromic hearing impairment.
Authors: Wu, S. / Hei, Z. / Zheng, L. / Zhou, J. / Liu, Z. / Wang, J. / Fang, P.
History
DepositionMar 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 29, 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
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,41112
Polymers241,1454
Non-polymers2,2668
Water9,836546
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7066
Polymers120,5732
Non-polymers1,1334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-32 kcal/mol
Surface area38260 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7066
Polymers120,5732
Non-polymers1,1334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-34 kcal/mol
Surface area38100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.025, 152.025, 108.453
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 72 through 73 or (resid 74...
21(chain B and (resid 72 through 73 or (resid 74...
31(chain C and (resid 72 through 74 or (resid 75...
41(chain D and (resid 72 through 73 or (resid 74...

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
11ASPASPPROPRO(chain A and (resid 72 through 73 or (resid 74...AA72 - 734 - 5
12ASNASNASNASN(chain A and (resid 72 through 73 or (resid 74...AA746
13VALVALPROPRO(chain A and (resid 72 through 73 or (resid 74...AA71 - 5753 - 507
14VALVALPROPRO(chain A and (resid 72 through 73 or (resid 74...AA71 - 5753 - 507
15VALVALPROPRO(chain A and (resid 72 through 73 or (resid 74...AA71 - 5753 - 507
16VALVALPROPRO(chain A and (resid 72 through 73 or (resid 74...AA71 - 5753 - 507
17VALVALPROPRO(chain A and (resid 72 through 73 or (resid 74...AA71 - 5753 - 507
21ASPASPPROPRO(chain B and (resid 72 through 73 or (resid 74...BB72 - 734 - 5
22ASNASNASNASN(chain B and (resid 72 through 73 or (resid 74...BB746
23ASPASPPROPRO(chain B and (resid 72 through 73 or (resid 74...BB72 - 5754 - 507
24ASPASPPROPRO(chain B and (resid 72 through 73 or (resid 74...BB72 - 5754 - 507
25ASPASPPROPRO(chain B and (resid 72 through 73 or (resid 74...BB72 - 5754 - 507
26GLUGLUGLUGLU(chain B and (resid 72 through 73 or (resid 74...BB9224
27ASPASPPROPRO(chain B and (resid 72 through 73 or (resid 74...BB72 - 5754 - 507
28ASPASPPROPRO(chain B and (resid 72 through 73 or (resid 74...BB72 - 5754 - 507
29ASPASPPROPRO(chain B and (resid 72 through 73 or (resid 74...BB72 - 5754 - 507
210ASPASPPROPRO(chain B and (resid 72 through 73 or (resid 74...BB72 - 5754 - 507
211ASPASPPROPRO(chain B and (resid 72 through 73 or (resid 74...BB72 - 5754 - 507
31ASPASPASNASN(chain C and (resid 72 through 74 or (resid 75...CC72 - 744 - 6
32GLNGLNGLNGLN(chain C and (resid 72 through 74 or (resid 75...CC757
33VALVALPROPRO(chain C and (resid 72 through 74 or (resid 75...CC71 - 5753 - 507
34VALVALPROPRO(chain C and (resid 72 through 74 or (resid 75...CC71 - 5753 - 507
35VALVALPROPRO(chain C and (resid 72 through 74 or (resid 75...CC71 - 5753 - 507
36VALVALPROPRO(chain C and (resid 72 through 74 or (resid 75...CC71 - 5753 - 507
41ASPASPPROPRO(chain D and (resid 72 through 73 or (resid 74...DD72 - 734 - 5
42ASNASNASNASN(chain D and (resid 72 through 73 or (resid 74...DD746
43ASPASPPROPRO(chain D and (resid 72 through 73 or (resid 74...DD72 - 5754 - 507
44ASPASPPROPRO(chain D and (resid 72 through 73 or (resid 74...DD72 - 5754 - 507
45ASPASPPROPRO(chain D and (resid 72 through 73 or (resid 74...DD72 - 5754 - 507
46ASPASPPROPRO(chain D and (resid 72 through 73 or (resid 74...DD72 - 5754 - 507
47ASPASPPROPRO(chain D and (resid 72 through 73 or (resid 74...DD72 - 5754 - 507

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Components

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


Mass: 60286.277 Da / Num. of mol.: 4 / Mutation: Y145H
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-KAA / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / 5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE


Mass: 474.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H26N8O7S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Magnesium acetate tetrahydrate, 0.1 M sodium citrate (pH 6.0) and 14% (W/V) PEG 5000 MME.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 97279 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 44.79 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.052 / Rrim(I) all: 0.125 / Χ2: 1.037 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.595.60.5797540.8250.2640.6290.492100
2.59-2.695.50.45697170.8770.2130.5040.525100
2.69-2.825.30.34997000.9140.1670.3880.58499.3
2.82-2.965.70.27297090.9470.1240.2990.65199.6
2.96-3.155.90.20797330.9680.0930.2270.785100
3.15-3.395.80.15998110.9790.0720.1740.977100
3.39-3.735.40.12196720.9850.0570.1341.37599.2
3.73-4.2760.197340.9910.0440.1091.812100
4.27-5.385.70.08297410.9930.0370.091.87499.9
5.38-505.80.0697080.9960.0270.0661.20399.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bju

3bju


Resolution: 2.5→50 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 4973 5.12 %
Rwork0.1634 92205 -
obs0.1657 97178 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.4 Å2 / Biso mean: 48.3002 Å2 / Biso min: 25.87 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15873 0 152 546 16571
Biso mean--43.42 47.62 -
Num. residues----2004
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6044X-RAY DIFFRACTION7.694TORSIONAL
12B6044X-RAY DIFFRACTION7.694TORSIONAL
13C6044X-RAY DIFFRACTION7.694TORSIONAL
14D6044X-RAY DIFFRACTION7.694TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.58220.24654360.1983905897
2.5822-2.68550.26024820.20289265100
2.6855-2.80780.25355310.2019923199
2.8078-2.95580.24794740.19399232100
2.9558-3.14090.23935960.18719155100
3.1409-3.38340.2564860.18879361100
3.3834-3.72380.22125680.1674911599
3.7238-4.26240.16624830.1389278100
4.2624-5.36910.1694790.12839299100
5.3691-500.19934380.1616921199
Refinement TLS params.Method: refined / Origin x: 19.0371 Å / Origin y: -43.8922 Å / Origin z: -0.1938 Å
111213212223313233
T0.2717 Å2-0.0014 Å20.0018 Å2-0.3142 Å2-0.0313 Å2--0.3803 Å2
L0.035 °2-0.0043 °2-0.0055 °2-0.0609 °20.006 °2--0.4523 °2
S0.0241 Å °-0.0018 Å °-0 Å °-0.0014 Å °0.0018 Å °-0.0054 Å °-0.0033 Å °0.1296 Å °-0.0257 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA71 - 575
2X-RAY DIFFRACTION1allB72 - 575
3X-RAY DIFFRACTION1allC71 - 575
4X-RAY DIFFRACTION1allD72 - 575
5X-RAY DIFFRACTION1allE1 - 4
6X-RAY DIFFRACTION1allS1 - 601
7X-RAY DIFFRACTION1allF1 - 4

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