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- PDB-7f9b: Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-pro... -

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Basic information

Entry
Database: PDB / ID: 7f9b
TitleHomo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L95
ComponentsBifunctional glutamate/proline--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / LIGASE / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation ...regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / GAIT complex / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to type II interferon / RNA stem-loop binding / cellular response to insulin stimulus / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / WHEP-TRS domain / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain signature. ...Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / WHEP-TRS domain / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / 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 / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / 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 I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / 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) / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / S15/NS1, RNA-binding
Similarity search - Domain/homology
Chem-JE6 / PROLINE / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsManickam, Y. / Malhotra, N. / Sharma, A.
CitationJournal: Plos Pathog. / Year: 2023
Title: Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis.
Authors: Yogavel, M. / Bougdour, A. / Mishra, S. / Malhotra, N. / Chhibber-Goel, J. / Bellini, V. / Harlos, K. / Laleu, B. / Hakimi, M.A. / Sharma, A.
History
DepositionJul 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Nov 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: Bifunctional glutamate/proline--tRNA ligase
B: Bifunctional glutamate/proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,47816
Polymers115,0622
Non-polymers1,41714
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-84 kcal/mol
Surface area37400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.730, 90.960, 83.490
Angle α, β, γ (deg.)90.000, 110.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional glutamate/proline--tRNA ligase / Bifunctional aminoacyl-tRNA synthetase / Cell proliferation-inducing gene 32 protein / Glutamatyl- ...Bifunctional aminoacyl-tRNA synthetase / Cell proliferation-inducing gene 32 protein / Glutamatyl-prolyl-tRNA synthetase


Mass: 57530.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli)
References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase

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Non-polymers , 6 types, 280 molecules

#2: 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.1 M HEPES, 1.5 M CaCl2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9799 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.995→45.48 Å / Num. obs: 66905 / % possible obs: 98.4 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.127 / Net I/σ(I): 9.9
Reflection shellResolution: 1.995→2.11 Å / Rmerge(I) obs: 0.928 / Num. unique obs: 10924 / Rrim(I) all: 1.008 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VAD

5vad


Resolution: 1.995→45.48 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 3328 5.01 %
Rwork0.1891 63162 -
obs0.1914 66490 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.53 Å2 / Biso mean: 47.0135 Å2 / Biso min: 26.03 Å2
Refinement stepCycle: final / Resolution: 1.995→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7600 0 67 266 7933
Biso mean--41.53 48.3 -
Num. residues----970
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9953-2.02380.34591200.3012221381
2.0238-2.0540.34651350.2675257499
2.054-2.08610.30831400.2764264698
2.0861-2.12030.32191370.2717260199
2.1203-2.15680.34841360.2566261398
2.1568-2.1960.31461400.2581264999
2.196-2.23830.3041380.2563262299
2.2383-2.2840.29851390.2522264499
2.284-2.33360.28281390.2556263499
2.3336-2.38790.29181390.2516264099
2.3879-2.44760.30241380.2592262399
2.4476-2.51380.30361390.2488263799
2.5138-2.58780.28451390.2459265399
2.5878-2.67130.30081400.2382265599
2.6713-2.76670.35011400.2531265299
2.7667-2.87750.29141400.2274267099
2.8775-3.00840.24011390.2026263599
3.0084-3.1670.23541410.1826268699
3.167-3.36540.21331410.1762671100
3.3654-3.62510.20411400.15832656100
3.6251-3.98970.19571410.1452683100
3.9897-4.56660.17431400.13062672100
4.5666-5.75160.17951430.14062703100
5.7516-45.480.19581440.1706273099
Refinement TLS params.Method: refined / Origin x: 5.6991 Å / Origin y: -7.2818 Å / Origin z: 19.0673 Å
111213212223313233
T0.3265 Å20.0008 Å2-0.0014 Å2-0.3168 Å2-0.0144 Å2--0.3417 Å2
L0.4707 °20.0523 °20.1259 °2-0.495 °2-0.0572 °2--0.763 °2
S-0.0158 Å °-0.0051 Å °0.0254 Å °-0.0207 Å °0.0281 Å °0.0118 Å °0.0166 Å °0.0299 Å °0 Å °
Refinement TLS groupSelection details: all

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