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- PDB-7evu: Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase ... -

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Basic information

Entry
Database: PDB / ID: 7evu
TitleCo-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with HFG and JE6
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsTRANSLATION / Toxoplasma gondii / Prolyl tRNA Synthetase / Inhibitor-Bound Structural Comparison / Multi-drug
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II ...YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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)
Similarity search - Domain/homology
Chem-HFG / Chem-JE6 / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.697 Å
AuthorsMishra, S. / Malhotra, N. / Manickam, Y. / Sharma, A.
CitationJournal: Plos Pathog. / Year: 2022
Title: Double drugging of prolyl-tRNA synthetase provides a new paradigm for anti-infective drug development.
Authors: Manickam, Y. / Malhotra, N. / Mishra, S. / Babbar, P. / Dusane, A. / Laleu, B. / Bellini, V. / Hakimi, M.A. / Bougdour, A. / Sharma, A.
History
DepositionMay 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
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 / 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: Prolyl-tRNA synthetase (ProRS)
B: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6487
Polymers115,8752
Non-polymers1,7735
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-20 kcal/mol
Surface area39230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.754, 70.830, 76.036
Angle α, β, γ (deg.)92.160, 101.440, 115.610
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Prolyl-tRNA synthetase (ProRS)


Mass: 57937.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_057780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6JUK2
#2: Chemical ChemComp-HFG / 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one / Halofuginone


Mass: 414.681 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid, medication*YM
#3: Chemical ChemComp-JE6 / ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide


Mass: 374.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Morpheus G2

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.69→61.97 Å / Num. obs: 138636 / % possible obs: 96.9 % / Redundancy: 3.5 % / CC1/2: 0.989 / Net I/σ(I): 6
Reflection shellResolution: 1.69→1.73 Å / Num. unique obs: 6454 / CC1/2: 0.314

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Processing

Software
NameVersionClassification
PHENIX1.15rc2_3428refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6aa0

6aa0


Resolution: 1.697→54.24 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 6794 4.91 %
Rwork0.1949 131635 -
obs0.1964 138429 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.91 Å2 / Biso mean: 39.0209 Å2 / Biso min: 16.52 Å2
Refinement stepCycle: final / Resolution: 1.697→54.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7875 0 116 555 8546
Biso mean--28.67 45.38 -
Num. residues----964
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.697-1.71590.33842100.3193384684
1.7159-1.73610.34232290.2988430595
1.7361-1.75730.28562240.2629435996
1.7573-1.77950.27082190.2562430695
1.7795-1.80290.31682210.2457433295
1.8029-1.82760.25432220.2312435396
1.8276-1.85380.26782400.2183440696
1.8538-1.88140.27042390.2152427696
1.8814-1.91080.25792160.2072443796
1.9108-1.94220.22872080.2043433896
1.9422-1.97560.23442370.1975441397
1.9756-2.01160.25132260.1962433997
2.0116-2.05030.2252280.1988438797
2.0503-2.09210.23682370.1975441397
2.0921-2.13760.25812260.1878441597
2.1376-2.18730.22372130.1861435897
2.1873-2.2420.22912150.1838443997
2.242-2.30270.22032250.1837442397
2.3027-2.37040.22832390.1813445598
2.3704-2.44690.23112090.1895444198
2.4469-2.53440.23262350.1926442198
2.5344-2.63590.2522560.1991441098
2.6359-2.75580.24312340.2038439098
2.7558-2.90110.23832150.204449398
2.9011-3.08280.2212110.1999446998
3.0828-3.32080.21322140.1964447699
3.3208-3.6550.20642350.1892448699
3.655-4.18370.20912570.1821447899
4.1837-5.27030.20732260.1717449299
5.2703-54.240.22422280.2045447999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3526-0.4062-0.0451.1103-0.24771.1413-0.0521-0.056-0.05240.05030.08870.1479-0.0527-0.0692-0.03840.1709-0.0098-0.01260.14230.00210.17557.180921.2208-5.417
24.03491.3847-2.68271.8266-0.65253.96230.2089-0.1610.2016-0.27890.0063-0.2674-0.16490.6804-0.19030.3589-0.02610.00320.37060.03620.21325.210337.3834-30.267
33.8398-0.3919-0.04052.54110.26424.1777-0.03110.2919-0.09110.07680.060.29680.0734-0.28290.01240.24090.0367-0.01620.26870.03780.386-16.34632.4077-12.2721
42.5998-0.1206-0.74841.657-0.38232.8117-0.0857-0.3391-0.06340.26050.1349-0.0174-0.0559-0.0052-0.0450.2137-0.0028-0.0270.2088-0.00230.244827.764812.7877.4944
54.75732.407-1.57763.6057-1.48752.5421-0.20590.1256-0.6532-0.46230.0279-0.06490.3690.00360.19840.25840.01940.00350.2473-0.01890.310117.6523.2135-15.2578
62.2116-0.1697-0.06471.41680.29181.68480.06260.2928-0.23-0.14990.02140.05370.0250.0037-0.06860.1349-0.0045-0.01530.1594-0.01910.194321.57755.6012-13.9877
72.173-0.58810.2321.53070.2933.32270.09530.3495-0.08-0.2009-0.0323-0.17370.08130.1761-0.00550.1488-0.02650.02570.24-0.03270.256536.87956.5603-13.4447
82.7492-0.2242-0.50134.04631.5833.6290.1064-0.50340.50780.33660.143-0.05-0.5857-0.0764-0.21970.43510.01530.0050.371-0.07330.310732.319731.432118.7422
91.436-0.5891-1.06194.80172.15932.67280.1704-0.29110.5333-0.130.3082-1.0455-0.360.356-0.49780.3177-0.0996-0.04320.4103-0.1480.509545.811725.875310.6516
102.5324-0.7473-1.11014.10680.88286.1382-0.2301-0.1872-0.37560.29220.1042-0.02910.45310.0320.0870.29910.0438-0.0210.3344-0.01550.485748.1784-10.97741.1519
113.2525-0.757-0.6593.71430.22022.9479-0.03550.1380.0147-0.06380.0881-0.2862-0.02570.1012-0.01570.1668-0.0065-0.03910.2953-0.01850.355150.5522-6.0795-5.7834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 613 )A333 - 613
2X-RAY DIFFRACTION2chain 'A' and (resid 614 through 734 )A614 - 734
3X-RAY DIFFRACTION3chain 'A' and (resid 735 through 830 )A735 - 830
4X-RAY DIFFRACTION4chain 'B' and (resid 333 through 388 )B333 - 388
5X-RAY DIFFRACTION5chain 'B' and (resid 389 through 423 )B389 - 423
6X-RAY DIFFRACTION6chain 'B' and (resid 424 through 496 )B424 - 496
7X-RAY DIFFRACTION7chain 'B' and (resid 497 through 603 )B497 - 603
8X-RAY DIFFRACTION8chain 'B' and (resid 604 through 700 )B604 - 700
9X-RAY DIFFRACTION9chain 'B' and (resid 701 through 734 )B701 - 734
10X-RAY DIFFRACTION10chain 'B' and (resid 735 through 780 )B735 - 780
11X-RAY DIFFRACTION11chain 'B' and (resid 781 through 830 )B781 - 830

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