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- EMDB-43084: S. aureus TarL H300N in complex with CDP-ribitol (two tetramers w... -

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Basic information

Entry
Database: EMDB / ID: EMD-43084
TitleS. aureus TarL H300N in complex with CDP-ribitol (two tetramers with CHAPS micelle)
Map dataSharpened map
Sample
  • Complex: S. aureus TarL H300N with CDP-ribitol and CHAPS
    • Protein or peptide: TarL H300N
Keywordsglycosyltransferase / polymerase / monotopic / amphipathic / TRANSFERASE
Function / homology
Function and homology information


CDP-ribitol ribitolphosphotransferase / CDP-ribitol ribitolphosphotransferase activity / CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / cell wall organization / plasma membrane
Similarity search - Function
: / CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / : / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase
Similarity search - Domain/homology
Teichoic acid ribitol-phosphate polymerase TarL
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLi FKK / Strynadka NCJ / Worrall LJ
Funding support Canada, United States, 4 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
Canada Research Chairs Canada
CitationJournal: Sci Adv / Year: 2024
Title: Cryo-EM analysis of TarL, a polymerase in wall teichoic acid biogenesis central to virulence and antibiotic resistance.
Authors: Franco K K Li / Liam J Worrall / Robert T Gale / Eric D Brown / Natalie C J Strynadka /
Abstract: Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of ...Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of the WTA ribitol-phosphate chain is catalyzed by TarL, a member of the largely uncharacterized TagF-like family of membrane-associated enzymes. We report the cryo-electron microscopy structure of TarL, showing a tetramer that forms an extensive membrane-binding platform of monotopic helices. TarL is composed of an amino-terminal immunoglobulin-like domain and a carboxyl-terminal glycosyltransferase-B domain for ribitol-phosphate polymerization. The active site of the latter is complexed to donor substrate cytidine diphosphate-ribitol, providing mechanistic insights into the catalyzed phosphotransfer reaction. Furthermore, the active site is surrounded by electropositive residues that serve to retain the lipid-linked acceptor for polymerization. Our data advance general insight into the architecture and membrane association of the still poorly characterized monotopic membrane protein class and present molecular details of ribitol-phosphate polymerization that may aid in the design of new antimicrobials.
History
DepositionDec 10, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43084.png

Downloads & links

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Map

FileDownload / File: emd_43084.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 338.88 Å		1.32 Å/pix.
x 256 pix.
= 338.88 Å		1.32 Å/pix.
x 256 pix.
= 338.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.0018966921 - 1.9200747
Average (Standard dev.)0.0024610348 (±0.03688106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 338.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43084_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_43084_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_43084_half_map_2.map
AnnotationHalf map A
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : S. aureus TarL H300N with CDP-ribitol and CHAPS

EntireName: S. aureus TarL H300N with CDP-ribitol and CHAPS
Components
  • Complex: S. aureus TarL H300N with CDP-ribitol and CHAPS
    • Protein or peptide: TarL H300N

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Supramolecule #1: S. aureus TarL H300N with CDP-ribitol and CHAPS

SupramoleculeName: S. aureus TarL H300N with CDP-ribitol and CHAPS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Two tetramers with CHAPS micelle
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: TarL H300N

MacromoleculeName: TarL H300N / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVKSKIYIDK IYWERVQLFV EGHSENLDL EDSNFVLRNL T ETRTMKAN DVKIDGNQFV CR FNVAILD NGYYLPEDKY LLV NEQELD YIAQLNPDVI NDAY QNLKP EQEEEYNELE TQNGK INFL LQTYLKEFRK GGISKK TVY TVTPEISSDV NEFVLDV VV ...String:
MVKSKIYIDK IYWERVQLFV EGHSENLDL EDSNFVLRNL T ETRTMKAN DVKIDGNQFV CR FNVAILD NGYYLPEDKY LLV NEQELD YIAQLNPDVI NDAY QNLKP EQEEEYNELE TQNGK INFL LQTYLKEFRK GGISKK TVY TVTPEISSDV NEFVLDV VV TTPEVKSIYI VRKYKELR K YFRKQSFNTR QFIFKAIFN TTKFFHLKKG NTVLFTSDSR PTMSGNFEY IYNEMLRQNL D KKYDIHTV FKANITDRRG II DKFRLPY LLGKADYIFV DDF HPLIYT VRFRRSQEVI QVWN AVGAF KTVGFSRTGK KGGPF IDSL NHRSYTKAYV SSETDI PFY AEAFGIKEKN VVPTGVP RT DVLFDEAYAT QIKQEMED E LPIIKGKKVI LFAPTFRGS GHGTAHYPFF KIDFERLARY CEKNNAVVL FKMHPFVKNR L NIADKHKQ YFVDVSDFRE VN DILFITD LLISDYSSLI YEY AVFKKP MIFYAFDLED YITT RDFYE PYESFVPGKI VQSFD ALMD ALDNEDYEGE KVIPFL DKH FKYQDGRSSE RLVRNLF GS KLVPRGSAAA ALEHHHHH H HH

UniProtKB: Teichoic acid ribitol-phosphate polymerase TarL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration9.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHEPES
500.0 mMSodium chloride
6.5 mMCHAPS
GridMaterial: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 19380 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1341400
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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