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- PDB-7bbu: Crystal Structure of human Prolyl-tRNA synthetase in complex with... -

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Basic information

Entry
Database: PDB / ID: 7bbu
TitleCrystal Structure of human Prolyl-tRNA synthetase in complex with NCP26 and L-Proline
ComponentsBifunctional glutamate/proline--tRNA ligase
KeywordsLIGASE / inhibitor / protein biosynthesis / ATP binding / tRNA
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-MU5 / NITRATE ION / PROLINE / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å
AuthorsJohansson, C. / Tye, M. / Payne, N.C. / Mazitschek, R. / Krojer, T. / Oppermann, U.C.T.
CitationJournal: To Be Published
Title: Crystal Structure of human Prolyl-tRNA synthetase in complex with NCP26 and L-Proline
Authors: Johansson, C. / Tye, M. / Payne, N.C. / Mazitschek, R. / Krojer, T. / Oppermann, U.C.T.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Bifunctional glutamate/proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,65716
Polymers58,3931
Non-polymers1,26415
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint15 kcal/mol
Surface area20970 Å2
2
A: Bifunctional glutamate/proline--tRNA ligase
hetero molecules

A: Bifunctional glutamate/proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,31432
Polymers116,7852
Non-polymers2,52830
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7530 Å2
ΔGint12 kcal/mol
Surface area37600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.090, 87.090, 108.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1815-

CL

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Components

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Protein , 1 types, 1 molecules A

#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: 58392.727 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria)
References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase

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Non-polymers , 7 types, 140 molecules

#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-MU5 / ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-(piperidin-1-ylcarbonylamino)pyrazine-2-carboxamide


Mass: 365.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M NH4NO3, 5 mM L-Pro, 2mM NCP26

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.19→61.95 Å / Num. obs: 25083 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 41.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.329 / Rpim(I) all: 0.075 / Rrim(I) all: 0.338 / Net I/σ(I): 8.8 / Num. measured all: 505143 / Scaling rejects: 2
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
2.19-2.2518.34.0143360318400.3410.9564.1280.899.8
9.79-61.9516.50.05754783310.9990.0140.05941.599.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.12-2829refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K86

4k86


Resolution: 2.19→61.948 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1241 4.95 %
Rwork0.2057 23805 -
obs0.2071 25046 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.54 Å2 / Biso mean: 48.9392 Å2 / Biso min: 26.46 Å2
Refinement stepCycle: final / Resolution: 2.19→61.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 81 125 3954
Biso mean--52.52 46.91 -
Num. residues----480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023918
X-RAY DIFFRACTIONf_angle_d0.4715301
X-RAY DIFFRACTIONf_chiral_restr0.042580
X-RAY DIFFRACTIONf_plane_restr0.003693
X-RAY DIFFRACTIONf_dihedral_angle_d15.6812335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.19-2.27770.33971140.31612628
2.2777-2.38140.31451360.29392601
2.3814-2.50690.31951180.27182614
2.5069-2.6640.3071530.25422602
2.664-2.86970.25881380.25192619
2.8697-3.15840.23681320.21592659
3.1584-3.61540.22171330.20112640
3.6154-4.55490.22731480.16292673
4.5549-61.9480.18541690.17812769
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)
13.5915-0.8521-0.43283.2084-0.46721.946-0.1002-0.0487-0.3243-0.05960.0517-0.09670.18650.16570.02750.3001-0.0297-0.01780.29850.0040.270625.98819.7086-12.088
23.44320.3749-0.43467.2055-0.43181.4217-0.11450.0385-0.3597-0.2534-0.00330.31670.2451-0.23330.08480.3071-0.04650.01350.36540.00440.33910.678617.3743-2.0284
32.82850.1344-0.35720.7738-0.09181.2739-0.01130.07150.03660.00870.00680.1866-0.048-0.11490.00580.301-0.0153-0.03060.2801-0.02840.34954.435328.0369-13.644
46.83072.85056.67713.16092.89528.0693-0.470.32750.3610.32320.222-0.2144-0.42580.58370.21830.4314-0.0547-0.03830.3943-0.00460.413943.863432.2021-8.2655
56.78961.18133.35127.91552.74877.7145-0.2704-0.0543-0.03650.04650.00580.05240.1610.13420.22130.3050.0334-0.01080.35270.01110.298843.181226.5137-9.2965
67.95562.77340.06229.30191.5344.8852-0.24760.73790.79980.29640.0643-1.1677-0.72091.53240.29020.5937-0.1263-0.14120.87910.17010.685949.604536.1012-16.778
79.68813.78295.73433.13611.83114.7732-0.12650.601-0.0134-0.12540.1177-0.10740.04780.21080.01540.34770.01750.06740.3810.0110.34918.163625.8234-32.9133
88.52011.00460.72736.9844-0.51278.64930.11630.5818-0.0789-0.39090.11160.0382-0.1991-0.2497-0.23920.31920.0296-0.03930.4939-0.06890.30866.296224.5248-37.1326
93.22491.6185-1.339.91365.01144.0919-1.39292.78762.8407-1.7262-3.05717.8407-3.3366-6.81784.47840.46410.0902-0.10730.6287-0.16240.73154.640925.2143-13.1339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1012 through 1071 )A1012 - 1071
2X-RAY DIFFRACTION2chain 'A' and (resid 1072 through 1110 )A1072 - 1110
3X-RAY DIFFRACTION3chain 'A' and (resid 1111 through 1287 )A1111 - 1287
4X-RAY DIFFRACTION4chain 'A' and (resid 1288 through 1336 )A1288 - 1336
5X-RAY DIFFRACTION5chain 'A' and (resid 1337 through 1369 )A1337 - 1369
6X-RAY DIFFRACTION6chain 'A' and (resid 1370 through 1396 )A1370 - 1396
7X-RAY DIFFRACTION7chain 'A' and (resid 1397 through 1462 )A1397 - 1462
8X-RAY DIFFRACTION8chain 'A' and (resid 1463 through 1512 )A1463 - 1512
9X-RAY DIFFRACTION9chain 'A' and (resid 1801 through 1801 )A1801

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