[English] 日本語
Yorodumi
- EMDB-24249: Oxidized PheRS G318W from Salmonella enterica serovar Typhimurium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24249
TitleOxidized PheRS G318W from Salmonella enterica serovar Typhimurium
Map dataoxidized PheRS from Salmonella enterica serovar Typhimurium
Sample
  • Complex: apo-PheRS tetramer structure
    • Protein or peptide: Phenylalanine--tRNA ligase alpha subunit
    • Protein or peptide: Phenylalanine--tRNA ligase beta subunit
Function / homology
Function and homology information


phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA synthetase, class IIc, mitochondrial / 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 / tRNA synthetase B5 domain / B5 domain profile. ...Phenylalanyl-tRNA synthetase, class IIc, mitochondrial / 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 / 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 / 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 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsSrinivas P / Dunham CM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065183 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI106699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008602 United States
CitationJournal: Nucleic Acids Res / Year: 2021
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
DepositionJun 16, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7n8y
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24249.png

Downloads & links

-
Map

FileDownload / File: emd_24249.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoxidized PheRS from Salmonella enterica serovar Typhimurium
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.0088 / Movie #1: 0.013
Minimum - Maximum-0.09327989 - 0.14374422
Average (Standard dev.)-3.3943036e-06 (±0.0038418653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z266.240266.240266.240
α/β/γ90.00090.00090.000
start NX/NY/NZ484647
NX/NY/NZ97101117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0930.144-0.000

-
Supplemental data

-
Sample components

-
Entire : apo-PheRS tetramer structure

EntireName: apo-PheRS tetramer structure
Components
  • Complex: apo-PheRS tetramer structure
    • Protein or peptide: Phenylalanine--tRNA ligase alpha subunit
    • Protein or peptide: Phenylalanine--tRNA ligase beta subunit

-
Supramolecule #1: apo-PheRS tetramer structure

SupramoleculeName: apo-PheRS tetramer structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

-
Macromolecule #1: Phenylalanine--tRNA ligase alpha subunit

MacromoleculeName: 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: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 36.799645 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

-
Macromolecule #2: Phenylalanine--tRNA ligase beta subunit

MacromoleculeName: 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: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 87.484883 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 12.0 sec. / Average electron dose: 64.67 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3pco

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 204902

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more