1DKU

CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for the function of Bacillus subtilis phosphoribosyl-pyrophosphate synthetase.

Eriksen, T.A.Kadziola, A.Bentsen, A.K.Harlow, K.W.Larsen, S.

(2000) Nat.Struct.Mol.Biol. 7: 303-308

  • DOI: 10.1038/74069
  • Primary Citation of Related Structures:  1DKR

  • PubMed Abstract: 
  • Here we report the first three-dimensional structure of a phosphoribosylpyrophosphate (PRPP) synthetase. PRPP is an essential intermediate in several biosynthetic pathways. Structures of the Bacillus subtilis PRPP synthetase in complex with analogs o ...

    Here we report the first three-dimensional structure of a phosphoribosylpyrophosphate (PRPP) synthetase. PRPP is an essential intermediate in several biosynthetic pathways. Structures of the Bacillus subtilis PRPP synthetase in complex with analogs of the activator phosphate and the allosteric inhibitor ADP show that the functional form of the enzyme is a hexamer. The individual subunits fold into two domains, both of which resemble the type I phosphoribosyltransfereases. The active site is located between the two domains and includes residues from two subunits. Phosphate and ADP bind to the same regulatory site consisting of residues from three subunits of the hexamer. In addition to identifying residues important for binding substrates and effectors, the structures suggest a novel mode of allosteric regulation.


    Related Citations: 
    • Overexpression of the B. Subtilis Phosphoribosylpyrophosphate Synthetase and Crystallization of the Free Enzyme and its Substrate-Effector Complexes
      Bentsen, A.-K.,Larsen, T.A.,Kadziola, A.,Larsen, S.,Harlow, K.W.
      (1996) Proteins 24: 238


    Organizational Affiliation

    Center for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
A, B
317Bacillus subtilis (strain 168)Gene Names: prs
EC: 2.7.6.1
Find proteins for P14193 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P14193
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ABM
Query on ABM

Download SDF File 
Download CCD File 
A, B
METHYL PHOSPHONIC ACID ADENOSINE ESTER
ALPHA-METHYLENE ADENOSINE MONOPHOSPHATE
C11 H16 N5 O6 P
PXSSQXBLDTZHLF-IOSLPCCCSA-N
 Ligand Interaction
AP2
Query on AP2

Download SDF File 
Download CCD File 
A, B
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H17 N5 O9 P2
OLCWZBFDIYXLAA-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 115.650α = 90.00
b = 115.650β = 90.00
c = 106.410γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
ROTAVATAdata scaling
CCP4data scaling
TRUNCATEdata scaling
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description