Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106987.82 
• Atom Count: 6876 
• Residue Count: 978 
• Unique protein chains: 1

5MP7

Crystal structure of phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis

• DOI: 10.2210/pdb5MP7/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2016-12-16 Released: 2017-04-26 
• Deposition Author(s): Donini, S., Garavaglia, S., Ferraris, D.M., Miggiano, R., Mori, s., Shibayama, K., Rizzi, M.
• Funding Organization(s): EU 7th Framework Program 

---

Experimental Data Snapshot

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

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

• PubMed: 28419153 
• 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 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
Molecule	Chains	Sequence Length	Organism	Details
Ribose-phosphate pyrophosphokinase	A, C, B	326	Mycobacterium 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ACT	A, B, C	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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 = 85.292	α = 90.00
b = 85.292	β = 90.00
c = 249.791	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-12-16 
• Released Date: 2017-04-26 
• Deposition Author(s): Donini, S., Garavaglia, S., Ferraris, D.M., Miggiano, R., Mori, s., Shibayama, K., Rizzi, M.

---

Funding Organization	Location	Grant Number
EU 7th Framework Program	Italy	260872

Revision History 

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