Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 72.41 kDa 
• Atom Count: 4877 
• Residue Count: 613 
• Unique protein chains: 1

2H08

crystal structure of human phosphoribosyl pyrophosphate synthetase 1 mutant Y146M

• DOI: 10.2210/pdb2H08/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-05-14 Released: 2006-10-24 
• Deposition Author(s): Li, S., Peng, B., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.257 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Literature

Crystal structure of human phosphoribosylpyrophosphate synthetase 1 reveals a novel allosteric site

Li, S., Lu, Y., Peng, B., Ding, J.

(2007) Biochem J 401: 39-47

• PubMed: 16939420 
• DOI: 10.1042/BJ20061066
• Primary Citation of Related Structures:  
  2H08, 2H07, 2H06, 2HCR


• PubMed Abstract: 
  

PRPP (phosphoribosylpyrophosphate) is an important metabolite essential for nucleotide synthesis and PRS (PRPP synthetase) catalyses synthesis of PRPP from R5P (ribose 5-phosphate) and ATP. The enzymatic activity of PRS is regulated by phosphate ions, divalent metal cations and ADP. In the present study we report the crystal structures of recombinant human PRS1 in complexes with SO4(2-) ions alone and with ATP, Cd2+ and SO4(2-) ions respectively. The AMP moiety of ATP binds at the ATP-binding site, and a Cd2+ ion binds at the active site and in a position to interact with the beta- and gamma-phosphates of ATP. A SO4(2-) ion, an analogue of the activator phosphate, was found to bind at both the R5P-binding site and the allosteric site defined previously. In addi-tion, an extra SO4(2-) binds at a site at the dimer interface between the ATP-binding site and the allosteric site. Binding of this SO4(2-) stabilizes the conformation of the flexible loop at the active site, leading to the formation of the active, open conformation which is essential for binding of ATP and initiation of the catalytic reaction. This is the first time that structural stabilization at the active site caused by binding of an activator has been observed. Structural and biochemical data show that mutations of some residues at this site influence the binding of SO4(2-) and affect the enzymatic activity. The results in the present paper suggest that this new SO4(2-)-binding site is a second allosteric site to regulate the enzymatic activity which might also exist in other eukaryotic PRSs (except plant PRSs of class II), but not in bacterial PRSs.

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Organizational Affiliation: 

State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-phosphate pyrophosphokinase I	A, B	326	Homo sapiens	Mutation(s): 1  Gene Names: PRPS1 EC: 2.7.6.1
Find proteins for P60891 (Homo sapiens) Explore P60891  Go to UniProtKB:  P60891
NIH Common Fund Data Resources
PHAROS  P60891 GTEx  ENSG00000147224

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.257 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.914	α = 90
b = 169.914	β = 90
c = 61.706	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-14 
• Released Date: 2006-10-24 
Deposition Author(s): Li, S., Peng, B., Ding, J.

Revision History 

• Version 1.0: 2006-10-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance