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- PDB-5vad: Crystal structure of human Prolyl-tRNA synthetase (PRS) in comple... -

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Basic information

Entry
Database: PDB / ID: 5vad
TitleCrystal structure of human Prolyl-tRNA synthetase (PRS) in complex with inhibitor
ComponentsBifunctional glutamate/proline--tRNA ligase
KeywordsLIGASE/LIGASE inhibitor / aminoacyl-tRNA synthetase / ATP dependent / inhibitor / 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 / 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
C-terminal domain of ProRS / 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 ...C-terminal domain of ProRS / 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 / Translation Initiation Factor IF3 / Anticodon-binding 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. / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-91Y / PROLINE / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.36 Å
AuthorsOkada, K. / Skene, R.J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Discovery of a novel prolyl-tRNA synthetase inhibitor and elucidation of its binding mode to the ATP site in complex with l-proline.
Authors: Adachi, R. / Okada, K. / Skene, R. / Ogawa, K. / Miwa, M. / Tsuchinaga, K. / Ohkubo, S. / Henta, T. / Kawamoto, T.
History
DepositionMar 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references / Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)117,9018
Polymers116,8112
Non-polymers1,0906
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-69 kcal/mol
Surface area38600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.089, 92.278, 84.832
Angle α, β, γ (deg.)90.000, 111.180, 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: 58405.656 Da / Num. of mol.: 2 / Fragment: UNP residues 998-1512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli)
References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase
#2: Chemical ChemComp-91Y / 3-[(cyclohexanecarbonyl)amino]-N-(2,3-dihydro-1H-inden-2-yl)pyrazine-2-carboxamide


Mass: 364.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N4O2
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 500mM CaCl2, Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 41903 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Χ2: 1.004 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.37-2.412.80.660.944197
2.41-2.453.30.5920.9711100
2.45-2.53.70.5591.0161100
2.5-2.553.80.491.0611100
2.55-2.613.80.4111.0091100
2.61-2.673.80.3560.9951100
2.67-2.743.80.291.0431100
2.74-2.813.80.2381.0151100
2.81-2.893.80.2031.0061100
2.89-2.993.80.1550.9991100
2.99-3.093.80.1241.0041100
3.09-3.223.80.10.991100
3.22-3.363.80.0821.0221100
3.36-3.543.80.0670.9981100
3.54-3.763.70.0560.997199.9
3.76-4.053.70.0520.9961100
4.05-4.463.70.0490.999199.9
4.46-5.13.60.0520.996199.9
5.1-6.433.60.0521.0031100
6.43-503.60.0470.996199.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.36→19.93 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / SU B: 23.063 / SU ML: 0.265 / SU R Cruickshank DPI: 0.4583 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.458 / ESU R Free: 0.28 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 2113 5.1 %RANDOM
Rwork0.1958 ---
obs0.1991 39697 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 174.24 Å2 / Biso mean: 72.575 Å2 / Biso min: 27.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0.21 Å2
2---0.6 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 2.36→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 72 142 7849
Biso mean--50.14 59.61 -
Num. residues----963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197894
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.95610701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8345955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69724.124354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.785151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8771544
X-RAY DIFFRACTIONr_chiral_restr0.1020.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215960
LS refinement shellResolution: 2.359→2.419 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 134 -
Rwork0.307 2657 -
all-2791 -
obs--91.66 %
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)
14.4328-1.51530.22553.791-2.71823.9647-0.1539-1.104-0.1130.40460.082-0.0720.2325-0.10250.07190.2204-0.06280.01740.35170.05340.0376-20.60651.913339.4148
24.4508-0.50132.33611.1394-0.83372.6559-0.1674-0.89190.25250.0230.10550.1148-0.0237-0.77080.06190.0730.01640.04190.2582-0.05090.0736-41.450310.98324.0389
37.1676-3.46490.41753.6907-0.07231.75950.91290.4331-1.245-0.6175-0.4627-0.04910.4130.3261-0.45020.46090.1198-0.13110.1412-0.03190.5332-11.9526-16.844125.2025
47.6364-2.3716-1.38172.25230.27282.190.4277-0.2198-1.45980.0884-0.09460.09640.6679-0.1332-0.33320.4982-0.1074-0.23270.13260.18750.7655-29.535-20.084129.4773
53.333-4.82092.36357.9364-2.39118.3174-0.1281-0.8899-0.3230.64290.17560.3942-0.1319-1.0737-0.04750.5093-0.41860.20341.71110.33220.2889-51.275-0.602948.9799
66.9798-0.36751.22153.49041.45064.5168-0.0086-1.16620.05220.4323-0.10270.37330.0689-0.64610.11130.4395-0.15390.20770.97590.28120.305-53.1572-1.969642.4581
74.5014-0.43812.02641.1592-0.47812.7386-0.32570.44330.7483-0.0005-0.1416-0.4102-0.32120.71880.46730.101-0.07830.00450.19170.11850.2776-13.491717.471817.4574
87.08433.77235.62284.30563.67585.68920.25560.8152-0.0522-0.0405-0.15330.40470.34860.5129-0.10230.45010.05530.01480.3639-0.01360.2494-40.36116.9819-11.025
97.6275.24572.65027.4261.65911.5597-0.00231.1578-0.2623-0.4977-0.0244-0.4369-0.17180.74280.02670.51480.04230.14080.99140.02510.2056-22.848811.5379-14.1658
102.08051.9320.94723.9203-1.28652.8607-0.36290.84640.4941-0.39880.24780.1233-0.38480.65040.11521.0909-0.31320.07891.58660.89641.6461-3.97338.1371-0.5171
116.4645-1.45053.50486.22132.20443.95970.05650.88460.8396-0.5735-0.0012-0.7936-0.56690.5847-0.05540.5363-0.31190.19390.79410.49580.7083-1.72931.99030.3221
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1016 - 1050
2X-RAY DIFFRACTION2A1051 - 1287
3X-RAY DIFFRACTION3A1288 - 1388
4X-RAY DIFFRACTION4A1389 - 1426
5X-RAY DIFFRACTION5A1427 - 1460
6X-RAY DIFFRACTION6A1461 - 1512
7X-RAY DIFFRACTION7B1051 - 1287
8X-RAY DIFFRACTION8B1288 - 1388
9X-RAY DIFFRACTION9B1389 - 1426
10X-RAY DIFFRACTION10B1427 - 1460
11X-RAY DIFFRACTION11B1461 - 1512

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