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Basic information

Entry
Database: PDB / ID: 4tva
TitleUniversal Pathway for Post-Transfer Editing Reactions: Insight from Crystal structure of TthPheRS with Puromycine
Components
  • Phenylalanine--tRNA ligase alpha subunit
  • Phenylalanine--tRNA ligase beta subunit
KeywordsLIGASE/ANTIBIOTIC / puromycine / editing / tRNA / PheRS / LIGASE-ANTIBIOTIC complex
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain ...Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/4 domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / 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) / Nucleic acid-binding proteins / 3-Layer(bba) Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE / PUROMYCIN / Phenylalanine--tRNA ligase alpha subunit / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase beta subunit
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.597 Å
AuthorsSafro, M. / Klipcan, L. / Tworowski, D. / Peretz, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Universal pathway for posttransfer editing reactions: Insights from the crystal structure of TtPheRS with puromycin.
Authors: Tworowski, D. / Klipcan, L. / Peretz, M. / Moor, N. / Safro, M.G.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Oct 7, 2015Group: Experimental preparation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6674
Polymers126,0302
Non-polymers6372
Water3,153175
1
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules

A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,3338
Polymers252,0604
Non-polymers1,2734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area28580 Å2
ΔGint-113 kcal/mol
Surface area79870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.475, 173.475, 138.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21B-902-

HOH

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Components

#1: Protein Phenylalanine--tRNA ligase alpha subunit / Phenylalanyl-tRNA synthetase alpha subunit / PheRS


Mass: 39309.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P27001, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 86720.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: P27002, UniProt: Q5SGX1*PLUS, phenylalanine-tRNA ligase
#3: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Chemical ChemComp-PUY / PUROMYCIN / Puromycin


Type: RNA linking / Mass: 471.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N7O5 / Comment: antibiotic, inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.77 Å3/Da / Density % sol: 74.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE 28% OF SATURATION, 20 MM IMIDAZOLE, PH 7.7, 10 MM MGCL2, 1 MM NAN3
PH range: 7.5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.59→27.06 Å / Num. obs: 74123 / % possible obs: 99.72 % / Redundancy: 3.2 % / Net I/σ(I): 15.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1PYS

1pys


Resolution: 2.597→27.058 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 1935 2.71 %Random
Rwork0.2492 ---
obs0.2494 71443 96.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.597→27.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8250 0 46 175 8471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088520
X-RAY DIFFRACTIONf_angle_d1.45611579
X-RAY DIFFRACTIONf_dihedral_angle_d16.553191
X-RAY DIFFRACTIONf_chiral_restr0.1011241
X-RAY DIFFRACTIONf_plane_restr0.011545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5974-2.66230.41651340.37614961X-RAY DIFFRACTION97
2.6623-2.73420.41551420.35614934X-RAY DIFFRACTION97
2.7342-2.81460.29661380.3724949X-RAY DIFFRACTION96
2.8146-2.90540.32831330.36814893X-RAY DIFFRACTION96
2.9054-3.00910.36161350.35724878X-RAY DIFFRACTION95
3.0091-3.12940.35431340.34084848X-RAY DIFFRACTION95
3.1294-3.27160.3241350.30654929X-RAY DIFFRACTION96
3.2716-3.44370.32581390.27754941X-RAY DIFFRACTION97
3.4437-3.6590.26691410.27054988X-RAY DIFFRACTION97
3.659-3.94070.2351320.2464884X-RAY DIFFRACTION95
3.9407-4.33590.26541390.21784898X-RAY DIFFRACTION95
4.3359-4.95990.20511380.18755009X-RAY DIFFRACTION97
4.9599-6.23630.19331450.20385091X-RAY DIFFRACTION98
6.2363-27.05940.19891500.19335305X-RAY DIFFRACTION99

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