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- PDB-5v58: Crystal structure of human prolyl-tRNA synthetase in complex with... -

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Basic information

Entry
Database: PDB / ID: 5v58
TitleCrystal structure of human prolyl-tRNA synthetase in complex with Aze-SA
ComponentsBifunctional glutamate/proline--tRNA ligase
KeywordsLIGASE / aminoacyl-tRNA synthetase / non-proteinogenic amino acids
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 / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol ...regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / RNA stem-loop binding / GAIT complex / cellular response to type II interferon / cellular response to insulin stimulus / GTPase binding / protein-containing complex assembly / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
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-8X1 / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsZhou, H. / Song, Y. / Schimmel, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM23562 United States
CitationJournal: Nat Commun / Year: 2017
Title: Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.
Authors: Song, Y. / Zhou, H. / Vo, M.N. / Shi, Y. / Nawaz, M.H. / Vargas-Rodriguez, O. / Diedrich, J.K. / Yates, J.R. / Kishi, S. / Musier-Forsyth, K. / Schimmel, P.
History
DepositionMar 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5583
Polymers59,0631
Non-polymers4952
Water46826
1
A: Bifunctional glutamate/proline--tRNA ligase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)119,1176
Polymers118,1272
Non-polymers9904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4790 Å2
ΔGint-104 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.766, 86.766, 108.773
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: 59063.453 Da / Num. of mol.: 1
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-8X1 / 5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine


Mass: 429.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N7O7S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 9% PEG3350, 250 mM sodium nitrate, 100 mM 3-(1-pyridino)-1-propane sulfonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 14793 / % possible obs: 96.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.057 / Χ2: 0.963 / Net I/σ(I): 19
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.59-2.638.10.3376520.964186.5
2.63-2.6810.60.2280.85195.9
2.68-2.7310.70.2130.904196
2.73-2.7910.50.1920.873196.5
2.79-2.8510.60.1720.921196.7
2.85-2.9210.50.1640.932196.9
2.92-2.9910.60.1280.949197.1
2.99-3.0710.60.1130.972196.9
3.07-3.1610.50.1011.027197.3
3.16-3.2610.60.0861.07197.2
3.26-3.3810.50.0760.98197.5
3.38-3.5110.50.0611.044197.3
3.51-3.6710.30.0560.917198.4
3.67-3.8710.20.050.916197.9
3.87-4.1110.10.0460.916197.8
4.11-4.439.60.0420.751198.4
4.43-4.879.60.0430.72197.4
4.87-5.589.90.0410.876198.7
5.58-7.0210.10.0411.116198.9
7.02-509.40.0531.503198.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HVC

4hvc


Resolution: 2.59→35.54 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.639 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.378 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.272 749 5.1 %RANDOM
Rwork0.2268 ---
obs0.2291 13977 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.51 Å2 / Biso mean: 59.398 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-1.33 Å2-0 Å2
2---1.33 Å2-0 Å2
3---4.3 Å2
Refinement stepCycle: final / Resolution: 2.59→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 30 26 3797
Biso mean--49.39 50.13 -
Num. residues----476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193868
X-RAY DIFFRACTIONr_bond_other_d0.0010.023604
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.9595257
X-RAY DIFFRACTIONr_angle_other_deg0.69538276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.165473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3424.023174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10815638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8461524
X-RAY DIFFRACTIONr_chiral_restr0.050.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02885
LS refinement shellResolution: 2.588→2.655 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 53 -
Rwork0.291 931 -
all-984 -
obs--89.78 %

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