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- PDB-7f99: Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-pro... -

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Basic information

Entry
Database: PDB / ID: 7f99
TitleHomo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96
ComponentsBifunctional glutamate/proline--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / MALARIA / INHIBITOR / PRS / 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-1UI / PROLINE / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 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 1.0Jul 6, 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)116,68915
Polymers115,0622
Non-polymers1,62713
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-79 kcal/mol
Surface area37680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.471, 91.518, 83.335
Angle α, β, γ (deg.)90.000, 110.110, 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, 420 molecules

#2: Chemical ChemComp-1UI / 4-[(3S)-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(5-methoxypyridin-3-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide


Mass: 499.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26FN5O3 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#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.: 407 / 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: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 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: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.979→78.252 Å / Num. obs: 69229 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 1 / Rrim(I) all: 0.121 / Net I/σ(I): 9.5
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 6.6 % / Num. unique obs: 3404 / CC1/2: 0.5 / Rrim(I) all: 0.854 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VAD

5vad


Resolution: 1.979→78.252 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 3366 4.87 %
Rwork0.1813 65821 -
obs0.1836 69187 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.81 Å2 / Biso mean: 43.1434 Å2 / Biso min: 16.16 Å2
Refinement stepCycle: final / Resolution: 1.979→78.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7657 0 83 415 8155
Biso mean--35.11 44.87 -
Num. residues----974
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9794-2.00770.36741350.2883267298
2.0077-2.03770.29761390.27792745100
2.0377-2.06950.2931430.2552743100
2.0695-2.10340.31451590.25912692100
2.1034-2.13970.3021500.24882763100
2.1397-2.17860.31941330.23572719100
2.1786-2.22050.31541230.22312752100
2.2205-2.26580.24981340.21722709100
2.2658-2.31510.26281430.21162755100
2.3151-2.3690.2551120.21112749100
2.369-2.42820.26831490.19412736100
2.4282-2.49390.25871320.19552737100
2.4939-2.56730.23761330.20042732100
2.5673-2.65010.23911220.20482750100
2.6501-2.74490.24411310.20082794100
2.7449-2.85480.22831240.20362739100
2.8548-2.98470.26311610.20612718100
2.9847-3.14210.23261460.1942736100
3.1421-3.33890.25591510.18272757100
3.3389-3.59670.22331590.16182722100
3.5967-3.95870.16991470.14612767100
3.9587-4.53140.1761530.12612734100
4.5314-5.70890.18431290.13512786100
5.7089-78.2520.20981580.17862814100
Refinement TLS params.Method: refined / Origin x: 5.9905 Å / Origin y: -6.8841 Å / Origin z: 18.5215 Å
111213212223313233
T0.1592 Å20.0058 Å20.0016 Å2-0.1706 Å2-0.0207 Å2--0.1882 Å2
L0.6203 °20.0723 °20.1787 °2-0.7629 °20.0464 °2--1.0394 °2
S-0.012 Å °0.0258 Å °-0.0127 Å °-0.0139 Å °0.0025 Å °0.0419 Å °0.0247 Å °0.0125 Å °0.0033 Å °
Refinement TLS groupSelection details: all

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