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- PDB-7osy: Human Prolyl-tRNA Synthetase in Complex with L-proline -

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Basic information

Entry
Database: PDB / ID: 7osy
TitleHuman Prolyl-tRNA Synthetase in Complex with L-proline
ComponentsBifunctional glutamate/proline--tRNA ligase
KeywordsLIGASE / beta barrel / tRNA synthetase / protein-ligand 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 / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / glutamyl-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 / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / glutamyl-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 / cytosol / cytoplasm
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
PROLINE / STRONTIUM ION / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsPang, L. / Zitko, J. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G077814N Belgium
Research Foundation - Flanders (FWO)G0A4616N Belgium
Research Foundation - Flanders (FWO)1S53516N Belgium
CitationJournal: Int J Mol Sci / Year: 2021
Title: Towards Novel 3-Aminopyrazinamide-Based Prolyl-tRNA Synthetase Inhibitors: In Silico Modelling, Thermal Shift Assay and Structural Studies.
Authors: Pang, L. / Weeks, S.D. / Juhas, M. / Strelkov, S.V. / Zitko, J. / Van Aerschot, A.
History
DepositionJun 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: 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)117,06212
Polymers116,1752
Non-polymers88710
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-176 kcal/mol
Surface area37780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.890, 88.404, 83.745
Angle α, β, γ (deg.)90.000, 110.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 58087.375 Da / Num. of mol.: 2 / Fragment: Prolyl-tRNA synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Plasmid: pETRUK / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS
References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase
#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2 / 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-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Sr
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: The purified protein at 30 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was incubated with 10 mM L-proline and 12% (v/v) DMSO on ice for 1 hr. Crystals were grown in a ...Details: The purified protein at 30 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was incubated with 10 mM L-proline and 12% (v/v) DMSO on ice for 1 hr. Crystals were grown in a Terasaki Microbatch plate by mixing 1 uL the pre-mix with 1 uL of reservoir solution containing 0.25-0.4 M SrCl2, 15-20% (v/v) PEG3350 and 100 mM HEPES pH 7.5. The drops were covered with paraffin oil. Crystals were flash frozen in liquid nitrogen directly from the plate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.2→78.59 Å / Num. obs: 47590 / % possible obs: 98.3 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.037 / Rrim(I) all: 0.082 / Net I/σ(I): 11.3 / Num. measured all: 226553
Reflection shell

Diffraction-ID: 1 / % possible all: 99.3

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.2-2.324.90.8643439869790.7130.4290.9671.9
6.96-78.594.40.033701615770.9990.0170.03832.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VAD

5vad


Resolution: 2.23→44.2 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 1940 4.23 %
Rwork0.2091 43882 -
obs0.2112 45822 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190 Å2 / Biso mean: 63.5721 Å2 / Biso min: 24.31 Å2
Refinement stepCycle: final / Resolution: 2.23→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7502 0 24 127 7653
Biso mean--50.41 52.88 -
Num. residues----967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.290.31191350.26843144327999
2.29-2.350.33251640.26243155331999
2.35-2.420.32371590.26173117327699
2.42-2.490.31791380.25223154329299
2.49-2.580.33681390.23913156329599
2.58-2.690.27121520.23563149330199
2.69-2.810.24521110.22873146325799
2.81-2.960.30861330.2283184331799
2.96-3.140.29041290.22213084321397
3.14-3.390.26481180.20952797291587
3.39-3.730.25321380.19643120325898
3.73-4.260.22911550.178131813336100
4.26-5.370.21330.169732363369100
5.37-44.20.27611360.2263259339599
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)
13.01590.59961.38421.5505-0.29353.3122-0.20720.1780.3132-0.00010.03950.2404-0.4214-0.16670.19380.25170.06470.02260.2744-0.00580.41716.425730.378521.9052
21.9470.1330.70740.8923-0.08491.3878-0.1985-0.23690.27030.11730.01110.187-0.1989-0.20950.14620.31410.03590.03520.355-0.0690.38443.164529.397739.2004
32.64480.92010.95792.82110.1781.815-0.21130.44790.1108-0.3480.1399-0.0997-0.14940.08640.08490.2757-0.03860.06720.4280.01780.266317.73824.692112.6456
43.87772.12590.88533.05211.50321.6509-0.15370.6995-0.3597-0.14390.2406-0.30930.08450.4215-0.10160.28260.0160.05230.5408-0.03640.404630.976717.991112.6408
55.48271.9114-1.81866.1786-2.56313.86290.5551-0.136-0.66630.6975-0.43660.29770.2009-0.573-0.10920.5756-0.26330.02530.5834-0.08880.5719-2.2101-5.734613.5027
66.22153.6657-3.21554.2328-2.45724.1867-0.32631.1249-0.4033-0.94210.2487-0.34350.320.06390.13820.67230.0810.09830.8539-0.15710.601530.36427.7353-3.6916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1016 through 1151 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1152 through 1512 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 1016 through 1178 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 1179 through 1287 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1288 through 1394 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1395 through 1512 )B0

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