5AYY

CRYSTAL STRUCTURE OF HUMAN QUINOLINATE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH THE REACTANT QUINOLINATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis

Youn, H.S.Kim, T.G.Kim, M.K.Kang, G.B.Kang, J.Y.Lee, J.G.An, J.Y.Park, K.R.Lee, Y.Im, Y.J.Lee, J.H.Eom, S.H.

(2016) Sci Rep 6: 19681-19681

  • DOI: 10.1038/srep19681
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Quinolinate phosphoribosyltransferase (QPRT) catalyses the production of nicotinic acid mononucleotide, a precursor of de novo biosynthesis of the ubiquitous coenzyme nicotinamide adenine dinucleotide. QPRT is also essential for maintaining the homeo ...

    Quinolinate phosphoribosyltransferase (QPRT) catalyses the production of nicotinic acid mononucleotide, a precursor of de novo biosynthesis of the ubiquitous coenzyme nicotinamide adenine dinucleotide. QPRT is also essential for maintaining the homeostasis of quinolinic acid in the brain, a possible neurotoxin causing various neurodegenerative diseases. Although QPRT has been extensively analysed, the molecular basis of the reaction catalysed by human QPRT remains unclear. Here, we present the crystal structures of hexameric human QPRT in the apo form and its complexes with reactant or product. We found that the interaction between dimeric subunits was dramatically altered during the reaction process by conformational changes of two flexible loops in the active site at the dimer-dimer interface. In addition, the N-terminal short helix α1 was identified as a critical hexamer stabilizer. The structural features, size distribution, heat aggregation and ITC studies of the full-length enzyme and the enzyme lacking helix α1 strongly suggest that human QPRT acts as a hexamer for cooperative reactant binding via three dimeric subunits and maintaining stability. Based on our comparison of human QPRT structures in the apo and complex forms, we propose a drug design strategy targeting malignant glioma.


    Organizational Affiliation

    Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, South Korea.,School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,College of Pharmacy, Chonnam National University, Gwangju 500-757, South Korea.,Department of Polar Sciences, Korea University of Science and Technology, Incheon 406-840, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinate-nucleotide pyrophosphorylase [carboxylating]
A, B, C, D, E, F, G, H, I
305Homo sapiensMutation(s): 0 
Gene Names: QPRT
EC: 2.4.2.19
Find proteins for Q15274 (Homo sapiens)
Go to Gene View: QPRT
Go to UniProtKB:  Q15274
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NTM
Query on NTM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
QUINOLINIC ACID
C7 H5 N O4
GJAWHXHKYYXBSV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 174.245α = 90.00
b = 174.245β = 90.00
c = 211.684γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2020-01-29
    Type: Derived calculations, Structure summary