6ASV

E. coli PRPP Synthetase

• PDB DOI: https://doi.org/10.2210/pdb6ASV/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-25 Released: 2019-01-23 
• Deposition Author(s): French, J.B., Zhou, W.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.212 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

Crystal structure of E. coli PRPP synthetase.

Zhou, W., Tsai, A., Dattmore, D.A., Stives, D.P., Chitrakar, I., D'alessandro, A.M., Patil, S., Hicks, K.A., French, J.B.

(2019) BMC Struct Biol 19: 1-1

• PubMed: 30646888 
• DOI: https://doi.org/10.1186/s12900-019-0100-4
• Primary Citation of Related Structures:  
  6ASV


• PubMed Abstract: 
  

  Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) is an enzyme that catalyzes the ATP-dependent conversion of ribose-5-phosphate to phosphoribosyl pyrophosphate. The reaction product is a key precursor for the biosynthesis of purine and pyrimidine nucleotides.

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Organizational Affiliation: 

Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 109.92 kDa 
• Atom Count: 7,225 
• Modelled Residue Count: 919 
• Deposited Residue Count: 1,005 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-phosphate pyrophosphokinase	A, B, C	335	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: prs, prsA, Z1978, ECs1712 EC: 2.7.6.1
UniProt
Find proteins for P0A717 (Escherichia coli (strain K12)) Explore P0A717  Go to UniProtKB:  P0A717

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth A], G [auth B], H [auth B], J [auth C], K [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.212 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.757	α = 90
b = 138.436	β = 90
c = 137.438	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
HKL-2000	data processing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): French, J.B., Zhou, W.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1455596

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description