[English] 日本語
![](img/lk-miru.gif)
- EMDB-24249: Oxidized PheRS G318W from Salmonella enterica serovar Typhimurium -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-24249 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Oxidized PheRS G318W from Salmonella enterica serovar Typhimurium | ||||||||||||
![]() | oxidized PheRS from Salmonella enterica serovar Typhimurium | ||||||||||||
![]() |
| ||||||||||||
![]() | synthetase / tRNA-binding protein / tetrameric / oxidized / RNA BINDING PROTEIN / LIGASE | ||||||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.65 Å | ||||||||||||
![]() | Srinivas P / Dunham CM | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 59.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 13 KB 13 KB | Display Display | ![]() |
Images | ![]() | 99.5 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n8yMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | oxidized PheRS from Salmonella enterica serovar Typhimurium | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : apo-PheRS tetramer structure
Entire | Name: apo-PheRS tetramer structure |
---|---|
Components |
|
-Supramolecule #1: apo-PheRS tetramer structure
Supramolecule | Name: apo-PheRS tetramer structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() |
-Macromolecule #1: Phenylalanine--tRNA ligase alpha subunit
Macromolecule | Name: Phenylalanine--tRNA ligase alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: phenylalanine-tRNA ligase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 36.799645 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSHLAELVAN AAAAINQASD VAALDNVRVE YLGKKGHLTL QMTTLRDLPP EERPAAGAVI NAAKEQVQQA LNARKAELES AALNARLAA ETIDISLPGR RIENGGLHPV TRTIDRIESF FGELGFTVAT GPEIEDDYHN FDALNIPGHH PARADHDTFW F DATRLLRT ...String: MSHLAELVAN AAAAINQASD VAALDNVRVE YLGKKGHLTL QMTTLRDLPP EERPAAGAVI NAAKEQVQQA LNARKAELES AALNARLAA ETIDISLPGR RIENGGLHPV TRTIDRIESF FGELGFTVAT GPEIEDDYHN FDALNIPGHH PARADHDTFW F DATRLLRT QTSGVQIRTM KAQQPPIRII APGRVYRNDY DQTHTPMFHQ MEGLIVDTNI SFTNLKGTLH DFLRNFFEED LQ IRFRPSY FPFTEPSAEV DVMGKNGKWL EVLGCGMVHP NVLRNVGIDP EIYSGFAFGM GMERLTMLRY GVTDLRSFFE NDL RFLKQF K UniProtKB: Phenylalanine--tRNA ligase alpha subunit |
-Macromolecule #2: Phenylalanine--tRNA ligase beta subunit
Macromolecule | Name: Phenylalanine--tRNA ligase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: phenylalanine-tRNA ligase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 87.484883 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKFSELWLRE WVNPAIDSDA LANQITMAGL EVDGVEPVAG SFNGVVVGEV VECAQHPNAD KLRVTKVNVG GERLLDIVCG APNCRQGLK VAVATIGAIL PGDFKIKAAK LRGEPSEGML CSFSELGISD DHSGIIELPA DAPLGTDIRE YLKLDDNTIE I SVTPNRAD ...String: MKFSELWLRE WVNPAIDSDA LANQITMAGL EVDGVEPVAG SFNGVVVGEV VECAQHPNAD KLRVTKVNVG GERLLDIVCG APNCRQGLK VAVATIGAIL PGDFKIKAAK LRGEPSEGML CSFSELGISD DHSGIIELPA DAPLGTDIRE YLKLDDNTIE I SVTPNRAD CLGIIGVARD VAVLNKAPLQ EPEMAPVTAT ISDTLPITVE AADACPRYLG RVVKGINVNA PTPLWMKEKL RR CGIRSID AVVDVTNYVL LELGQPMHAF DKDRIDGGIV VRMAKEGETV VLLDGSEATL NADTLVIADH HKALGIAGIF WGE HSGVNG ETQNVLLECA YFNPLSITGR ARRHGLHTDA SHRYERGVDP ALQYKAIERA TRLLLDICGG DAGPIIDVSN EATL PKRAT ITLRRSKLDR LIGHHIADEQ VSDILRRLGC EVTEGQDEWK AVAPTWRFDM EIEEDLVEEV ARVYGYNNIP DEPIQ AGLI MGTHREADLS LKRVKTMLND KGYQEVITYS FVDPKVQQLI HPGAEALLLP NPISVEMSAM RLSLWSGLLA TVVYNQ NRQ QNRVRIFETG LRFVPDTQAN LGIRQDLMLA GVICGNRYDE HWNLAKETVD FYDLKGDLEA VLDLTGKLGD IQFKAEM NP ALHPGQSAAI YLKDERIGFI GVVHPELERK LDLNGRTLVF ELEWNKLADR IVPQAREISR FPANRRDIAV VVAENVPA A DILSECKKVG VNQVVGVNLF DVYRGKGVAE GYKSLAISLI LQDTNRTLEE EEIAATVAKC VEALKERFQA SLRD UniProtKB: Phenylalanine--tRNA ligase beta subunit |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 12.0 sec. / Average electron dose: 64.67 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 204902 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |