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- PDB-7n8y: Oxidized PheRS G318W from Salmonella enterica serovar Typhimurium -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n8y | ||||||||||||
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Title | Oxidized PheRS G318W from Salmonella enterica serovar Typhimurium | ||||||||||||
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![]() | RNA BINDING PROTEIN / LIGASE / synthetase / tRNA-binding protein / tetrameric / oxidized | ||||||||||||
Function / homology | ![]() phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å | ||||||||||||
![]() | Srinivas, P. / Dunham, C.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy. Authors: Pooja Srinivas / Rebecca E Steiner / Ian J Pavelich / Ricardo Guerrero-Ferreira / Puneet Juneja / Michael Ibba / Christine M Dunham / ![]() Abstract: High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ...High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNAPhe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNAPhe, despite these oxidized residues not being directly implicated in PheRS activity. Here, we solve a 3.6 Å cryo-electron microscopy structure of oxidized S. Typhimurium PheRS. We find that oxidation results in widespread structural rearrangements in the β-subunit editing domain and enlargement of its editing domain. Oxidization also enlarges the phenylalanyl-adenylate binding pocket but to a lesser extent. Together, these changes likely explain why oxidation leads to hyperaccurate editing and decreased misincorporation of tyrosine. Taken together, these results help increase our understanding of the survival of S. Typhimurium during human infection. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 488.4 KB | Display | ![]() |
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PDB format | ![]() | 377.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 867 KB | Display | ![]() |
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Full document | ![]() | 889.4 KB | Display | |
Data in XML | ![]() | 56.7 KB | Display | |
Data in CIF | ![]() | 86.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24249MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 36799.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pheS / Production host: ![]() ![]() #2: Protein | Mass: 87484.883 Da / Num. of mol.: 2 / Mutation: G318W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pheT / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: apo-PheRS tetramer structure / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 12 sec. / Electron dose: 64.67 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204902 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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