1DKU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


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 Biol 7: 303-308

  • DOI: 10.1038/74069
  • Primary Citation of Related Structures:  
    1DKU, 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 of the activator phosphate and the allosteric inhibitor ADP show that the functional form of the enzyme is a hexamer ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)A, B317Bacillus subtilisMutation(s): 0 
EC: 2.7.6.1
UniProt
Find proteins for P14193 (Bacillus subtilis (strain 168))
Explore P14193 
Go to UniProtKB:  P14193
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AP2 (Subject of Investigation/LOI)
Query on AP2

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H17 N5 O9 P2
OLCWZBFDIYXLAA-IOSLPCCCSA-N
 Ligand Interaction
ABM (Subject of Investigation/LOI)
Query on ABM

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]METHYL PHOSPHONIC ACID ADENOSINE ESTER
C11 H16 N5 O6 P
PXSSQXBLDTZHLF-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.65α = 90
b = 115.65β = 90
c = 106.41γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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