5MP7

Crystal structure of phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biochemical and structural investigations on phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis.

Donini, S.Garavaglia, S.Ferraris, D.M.Miggiano, R.Mori, S.Shibayama, K.Rizzi, M.

(2017) PLoS ONE 12: e0175815-e0175815

  • DOI: 10.1371/journal.pone.0175815

  • PubMed Abstract: 
  • Mycobacterium smegmatis represents one model for studying the biology of its pathogenic relative Mycobacterium tuberculosis. The structural characterization of a M. tuberculosis ortholog protein can serve as a valid tool for the development of molecu ...

    Mycobacterium smegmatis represents one model for studying the biology of its pathogenic relative Mycobacterium tuberculosis. The structural characterization of a M. tuberculosis ortholog protein can serve as a valid tool for the development of molecules active against the M. tuberculosis target. In this context, we report the biochemical and structural characterization of M. smegmatis phosphoribosylpyrophosphate synthetase (PrsA), the ortholog of M. tuberculosis PrsA, the unique enzyme responsible for the synthesis of phosphoribosylpyrophosphate (PRPP). PRPP is a key metabolite involved in several biosynthetic pathways including those for histidine, tryptophan, nucleotides and decaprenylphosphoryl-arabinose, an essential precursor for the mycobacterial cell wall biosynthesis. Since M. tuberculosis PrsA has been validated as a drug target for the development of antitubercular agents, the data presented here will add to the knowledge of the mycobacterial enzyme and could contribute to the development of M. tuberculosis PrsA inhibitors of potential pharmacological interest.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, Novara, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribose-phosphate pyrophosphokinase
A, C, B
326Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: prs
EC: 2.7.6.1
Find proteins for A0R3C8 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R3C8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.292α = 90.00
b = 85.292β = 90.00
c = 249.791γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
EU 7th Framework ProgramItaly260872

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Advisory, Data collection, Derived calculations