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- PDB-7rou: Structure of human tyrosyl tRNA synthetase in complex with ML901-Tyr -

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Basic information

Entry
Database: PDB / ID: 7rou
TitleStructure of human tyrosyl tRNA synthetase in complex with ML901-Tyr
ComponentsTyrosine--tRNA ligase, cytoplasmic
KeywordsLIGASE / enzyme / tyrosyl-tRNA synthetase / malaria / inhibitor / tyrosine-AMP
Function / homology
Function and homology information


interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / small molecule binding / response to starvation / tRNA binding / nuclear body / apoptotic process ...interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / small molecule binding / response to starvation / tRNA binding / nuclear body / apoptotic process / RNA binding / extracellular space / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Tyrosine-tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Chem-66I / Tyrosine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMetcalfe, R.D. / Xie, S.C. / Morton, C.J. / Tilley, L. / Griffin, M.D.W.
Funding support Japan, Australia, 2items
OrganizationGrant numberCountry
Global Health Innovative Technology FundGHIT-RFP-HTLP-H2019-104 Japan
National Health and Medical Research Council (NHMRC, Australia)APP1171794 Australia
CitationJournal: Science / Year: 2022
Title: Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy.
Authors: Xie, S.C. / Metcalfe, R.D. / Dunn, E. / Morton, C.J. / Huang, S.C. / Puhalovich, T. / Du, Y. / Wittlin, S. / Nie, S. / Luth, M.R. / Ma, L. / Kim, M.S. / Pasaje, C.F.A. / Kumpornsin, K. / ...Authors: Xie, S.C. / Metcalfe, R.D. / Dunn, E. / Morton, C.J. / Huang, S.C. / Puhalovich, T. / Du, Y. / Wittlin, S. / Nie, S. / Luth, M.R. / Ma, L. / Kim, M.S. / Pasaje, C.F.A. / Kumpornsin, K. / Giannangelo, C. / Houghton, F.J. / Churchyard, A. / Famodimu, M.T. / Barry, D.C. / Gillett, D.L. / Dey, S. / Kosasih, C.C. / Newman, W. / Niles, J.C. / Lee, M.C.S. / Baum, J. / Ottilie, S. / Winzeler, E.A. / Creek, D.J. / Williamson, N. / Parker, M.W. / Brand, S. / Langston, S.P. / Dick, L.R. / Griffin, M.D.W. / Gould, A.E. / Tilley, L.
History
DepositionAug 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3679
Polymers41,1191
Non-polymers1,2488
Water5,332296
1
A: Tyrosine--tRNA ligase, cytoplasmic
hetero molecules

A: Tyrosine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,73518
Polymers82,2392
Non-polymers2,49616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4650 Å2
ΔGint-143 kcal/mol
Surface area29620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.622, 162.189, 35.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-591-

HOH

21A-678-

HOH

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Components

#1: Protein Tyrosine--tRNA ligase, cytoplasmic / Tyrosyl-tRNA synthetase / TyrRS


Mass: 41119.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YARS1, YARS / Production host: Escherichia coli (E. coli) / References: UniProt: P54577, tyrosine-tRNA ligase
#2: Chemical ChemComp-66I / {(2R,3S,4R,5R)-5-[4-amino-3-(difluoromethoxy)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-dihydroxyoxolan-2-yl}methyl [(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]sulfamate (non-preferred name)


Mass: 575.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23F2N7O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.1-2.3 M ammonium sulfate, 2% acetone, 0.1 M NaH2PO4/K2HPO4, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→43.98 Å / Num. obs: 48890 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 33.35 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Rsym value: 0.081 / Net I/σ(I): 13.6
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2547 / CC1/2: 0.467 / Rpim(I) all: 1.147 / Rrim(I) all: 3.024 / Rsym value: 2.795

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QBT

4qbt


Resolution: 1.7→43.98 Å / SU ML: 0.2134 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 23.2572
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 2395 4.91 %
Rwork0.1782 46420 -
obs0.1797 48815 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.94 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 74 296 3047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032819
X-RAY DIFFRACTIONf_angle_d1.0863820
X-RAY DIFFRACTIONf_chiral_restr0.0662421
X-RAY DIFFRACTIONf_plane_restr0.0077474
X-RAY DIFFRACTIONf_dihedral_angle_d16.7221053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.36911210.33412691X-RAY DIFFRACTION99.93
1.73-1.770.34511470.29912692X-RAY DIFFRACTION100
1.77-1.810.2841350.2722672X-RAY DIFFRACTION99.96
1.81-1.860.29231310.25712721X-RAY DIFFRACTION100
1.86-1.910.3141400.23812644X-RAY DIFFRACTION99.96
1.91-1.970.24451460.2272732X-RAY DIFFRACTION100
1.97-2.030.22681320.21992688X-RAY DIFFRACTION100
2.03-2.10.21521440.18682713X-RAY DIFFRACTION100
2.1-2.190.2621390.1742698X-RAY DIFFRACTION100
2.19-2.280.22251290.17972714X-RAY DIFFRACTION100
2.29-2.410.22491500.17762698X-RAY DIFFRACTION99.93
2.41-2.560.22921440.1792738X-RAY DIFFRACTION100
2.56-2.750.20321300.19292742X-RAY DIFFRACTION100
2.75-3.030.23861560.19882736X-RAY DIFFRACTION100
3.03-3.470.20341450.17782790X-RAY DIFFRACTION99.97
3.47-4.370.16541530.14292796X-RAY DIFFRACTION99.97
4.37-43.980.19051530.16192955X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: 60.5914104558 Å / Origin y: 22.236189405 Å / Origin z: 42.3382386403 Å
111213212223313233
T0.291135479088 Å20.0102263751383 Å2-0.0180006851083 Å2-0.249328110361 Å2-0.0280965244989 Å2--0.277066202072 Å2
L1.69099533481 °2-1.39077528517 °2-0.55578068253 °2-1.82517536212 °20.485723078738 °2--0.985754002049 °2
S-0.0298933717209 Å °0.0859979948981 Å °-0.114861222758 Å °-0.00367683116469 Å °-0.0768133862127 Å °0.196666492852 Å °-0.0235477047496 Å °-0.0907130235413 Å °0.0988288342313 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 4 through 342)

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