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- PDB-7osz: Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 4d -

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Basic information

Entry
Database: PDB / ID: 7osz
TitleHuman Prolyl-tRNA Synthetase in Complex with L-proline and Compound 4d
ComponentsBifunctional glutamate/proline--tRNA ligase
KeywordsLIGASE / beta barrel / tRNA synthetase / protein-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 / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / 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 / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / GAIT complex / 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 / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain ...Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / 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-0X7 / PROLINE / STRONTIUM ION / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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)117,63415
Polymers116,1752
Non-polymers1,45913
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-193 kcal/mol
Surface area37250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.671, 86.696, 83.117
Angle α, β, γ (deg.)90.000, 110.140, 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: 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

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Non-polymers , 5 types, 93 molecules

#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-0X7 / 3-[(2-methylphenyl)methylamino]pyrazine-2-carboxamide


Mass: 242.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Sr
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.03 Å3/Da / Density % sol: 39.37 %
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, 2 mM compound and 12% (v/v) DMSO on ice for 1 hr. Crystals were ...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, 2 mM compound 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: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.46→78.03 Å / Num. obs: 33733 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.065 / Rrim(I) all: 0.126 / Net I/σ(I): 7 / Num. measured all: 124080 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.46-2.593.80.861875749200.7270.5091.0031.599.8
7.78-78.033.20.041347110990.9970.0260.04918.498.4

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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: 2.46→78.03 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2777 1724 5.12 %
Rwork0.2201 31969 -
obs0.223 33693 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.65 Å2 / Biso mean: 62.8381 Å2 / Biso min: 22.92 Å2
Refinement stepCycle: final / Resolution: 2.46→78.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7505 0 61 80 7646
Biso mean--77.04 53.62 -
Num. residues----971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.46-2.530.39661540.315326332787100
2.53-2.610.36391380.295326362774100
2.61-2.710.35461440.281526702814100
2.71-2.820.36461350.254126592794100
2.82-2.940.32141420.249226682810100
2.94-3.10.31291360.22626742810100
3.1-3.290.29321660.212926262792100
3.29-3.550.27641590.21152641280099
3.55-3.90.26991300.18822691282199
3.9-4.470.23821370.1842679281699
4.47-5.630.22861330.1832676280999
5.63-78.030.26231500.24982716286699
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)
11.62470.489-0.17821.3472-1.1463.8591-0.12630.37650.21870.08690.04510.0226-0.50450.10440.08030.25440.04770.00360.42370.0430.35799.11732.775923.8538
21.3102-0.26710.62670.4013-0.09041.3332-0.11350.03190.10150.07280.06820.0544-0.1794-0.04580.07470.3130.01230.00610.4996-0.02570.39222.387828.846737.3751
31.77130.7583-0.05042.70610.71283.4781-0.0005-0.11340.3065-0.2705-0.0848-0.1785-0.0993-0.03470.07980.21710.01710.04570.49270.02910.38313.615719.91310.1307
41.21860.30660.36282.37110.23940.6666-0.0648-0.1120.02020.05860.0601-0.17090.03530.11960.03230.2842-0.02050.06880.71240.00670.362723.284125.958115.3038
51.17020.87580.72271.84591.5421.6267-0.1548-0.03680.0132-0.20690.10330.0343-0.16020.0805-0.00110.3288-0.0090.02320.7620.05540.498630.490919.883111.2852
63.18710.7887-0.85763.8787-0.84353.13270.0482-0.447-0.20430.04850.07740.07010.3809-0.5523-0.1240.3014-0.02950.00860.7205-0.00260.3907-2.7303-3.95114.1959
74.44312.447-1.75381.8025-1.07630.9511-0.08230.1239-0.4438-0.2833-0.0349-0.0750.0899-0.06650.13710.43910.01950.04390.6815-0.04930.543624.74633.6849-1.3246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1016 through 1122 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1123 through 1512 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 1015 through 1100 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 1101 through 1199 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1200 through 1287 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1288 through 1370 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1371 through 1512 )B0

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