+Open data
-Basic information
Entry | Database: PDB / ID: 8j8j | ||||||
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Title | Membrane bound PRTase, C3 symmetry, donor bound | ||||||
Components | Decaprenyl-phosphate phosphoribosyltransferase | ||||||
Keywords | MEMBRANE PROTEIN / phosphoribose transferase complex | ||||||
Function / homology | Function and homology information decaprenyl-phosphate phosphoribosyltransferase / arabinosyltransferase activity / glycolipid biosynthetic process / capsule polysaccharide biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / cell wall organization / transferase activity / magnesium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | ||||||
Authors | Wu, F.Y. / Gao, S. / Zhang, L. / Rao, Z.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Microbiol / Year: 2024 Title: Structural analysis of phosphoribosyltransferase-mediated cell wall precursor synthesis in Mycobacterium tuberculosis. Authors: Shan Gao / Fangyu Wu / Sudagar S Gurcha / Sarah M Batt / Gurdyal S Besra / Zihe Rao / Lu Zhang / Abstract: In Mycobacterium tuberculosis, Rv3806c is a membrane-bound phosphoribosyltransferase (PRTase) involved in cell wall precursor production. It catalyses pentosyl phosphate transfer from phosphoribosyl ...In Mycobacterium tuberculosis, Rv3806c is a membrane-bound phosphoribosyltransferase (PRTase) involved in cell wall precursor production. It catalyses pentosyl phosphate transfer from phosphoribosyl pyrophosphate to decaprenyl phosphate, to generate 5-phospho-β-ribosyl-1-phosphoryldecaprenol. Despite Rv3806c being an attractive drug target, structural and molecular mechanistic insight into this PRTase is lacking. Here we report cryogenic electron microscopy structures for Rv3806c in the donor- and acceptor-bound states. In a lipidic environment, Rv3806c is trimeric, creating a UbiA-like fold. Each protomer forms two helical bundles, which, alongside the bound lipids, are required for PRTase activity in vitro. Mutational and functional analyses reveal that decaprenyl phosphate and phosphoribosyl pyrophosphate bind the intramembrane and extramembrane cavities of Rv3806c, respectively, in a distinct manner to that of UbiA superfamily enzymes. Our data suggest a model for Rv3806c-catalysed phosphoribose transfer through an inverting mechanism. These findings provide a structural basis for cell wall precursor biosynthesis that could have potential for anti-tuberculosis drug development. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j8j.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j8j.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 8j8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j8j_validation.pdf.gz | 627.3 KB | Display | wwPDB validaton report |
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Full document | 8j8j_full_validation.pdf.gz | 643.2 KB | Display | |
Data in XML | 8j8j_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 8j8j_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/8j8j ftp://data.pdbj.org/pub/pdb/validation_reports/j8/8j8j | HTTPS FTP |
-Related structure data
Related structure data | 36071MC 8j8kC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 32682.355 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: Rv3806c Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WFR5, decaprenyl-phosphate phosphoribosyltransferase #2: Sugar | #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
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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 |
-Sample preparation
Component | Name: trimeric phosphoribosyltransferase / Type: COMPLEX / Details: trimeric phosphoribosyltransferase, donor bound / Entity ID: #1 / Source: MULTIPLE SOURCES | |||||||||||||||
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Molecular weight | Value: 0.0978 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono disperse | |||||||||||||||
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 9908 |
EM imaging optics | Energyfilter name: TFS Selectris |
-Processing
EM software |
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CTF correction | Details: CTF amplitude correction was performed following 3D reconstruction Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3597451 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 410532 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
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