8J8J

Membrane bound PRTase, C3 symmetry, donor bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analysis of phosphoribosyltransferase-mediated cell wall precursor synthesis in Mycobacterium tuberculosis.

Gao, S.Wu, F.Gurcha, S.S.Batt, S.M.Besra, G.S.Rao, Z.Zhang, L.

(2024) Nat Microbiol 9: 976-987

  • DOI: https://doi.org/10.1038/s41564-024-01643-8
  • Primary Citation of Related Structures:  
    8J8J, 8J8K

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Decaprenyl-phosphate phosphoribosyltransferaseA [auth D],
B [auth A],
C [auth B]
302Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv3806c
EC: 2.4.2.45
Membrane Entity: Yes 
UniProt
Find proteins for P9WFR5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFR5 
Go to UniProtKB:  P9WFR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFR5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGW
Query on PGW

Download Ideal Coordinates CCD File 
F [auth D],
I [auth A],
L [auth B]
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
PRP (Subject of Investigation/LOI)
Query on PRP

Download Ideal Coordinates CCD File 
D,
G [auth A],
J [auth B]
1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth D],
H [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)ChinaSRPG22-003

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Database references
  • Version 1.3: 2024-04-17
    Changes: Database references