3C2V

Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and the inhibitor phthalate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comprehensive X-ray Structural Studies of the Quinolinate Phosphoribosyl Transferase (BNA6) from Saccharomyces cerevisiae.

di Luccio, E.Wilson, D.K.

(2008) Biochemistry 47: 4039-4050

  • DOI: 10.1021/bi7020475
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Quinolinic acid phosphoribosyl transferase (QAPRTase, EC 2.4.2.19) is a 32 kDa enzyme encoded by the BNA6 gene in yeast and catalyzes the formation of nicotinate mononucleotide from quinolinate and 5-phosphoribosyl-1-pyrophosphate (PRPP). QAPRTase pl ...

    Quinolinic acid phosphoribosyl transferase (QAPRTase, EC 2.4.2.19) is a 32 kDa enzyme encoded by the BNA6 gene in yeast and catalyzes the formation of nicotinate mononucleotide from quinolinate and 5-phosphoribosyl-1-pyrophosphate (PRPP). QAPRTase plays a key role in the tryptophan degradation pathway via kynurenine, leading to the de novo biosynthesis of NAD (+) and clearing the neurotoxin quinolinate. To improve our understanding of the specificity of the eukaryotic enzyme and the course of events associated with catalysis, we have determined the crystal structures of the apo and singly bound forms with the substrates quinolinate and PRPP. This reveals that the enzyme folds in a manner similar to that of various prokaryotic forms which are approximately 30% identical in sequence. In addition, the structure of the Michaelis complex is approximated by PRPP and the quinolinate analogue phthalate bound to the active site. These results allow insight into the kinetic mechanism of QAPRTase and provide an understanding of structural diversity in the active site of the Saccharomyces cerevisiae enzyme when compared to prokaryotic homologues.


    Organizational Affiliation

    Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinate-nucleotide pyrophosphorylase
A
294Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BNA6 (QPT1)
EC: 2.4.2.19
Find proteins for P43619 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43619
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHT
Query on PHT

Download SDF File 
Download CCD File 
A
PHTHALIC ACID
C8 H6 O4
XNGIFLGASWRNHJ-UHFFFAOYSA-N
 Ligand Interaction
PRP
Query on PRP

Download SDF File 
Download CCD File 
A
ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PHTKd: 780000 nM BINDINGMOAD
PRPKd: 10100000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.225 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 154.668α = 90.00
b = 154.668β = 90.00
c = 69.346γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description