5AYY | pdb_00005ayy

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 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5AYY

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/srep19681
  • Primary Citation Related Structures: 
    5AYX, 5AYY, 5AYZ

  • 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 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
    • School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.

Macromolecule Content 

  • Total Structure Weight: 288.75 kDa 
  • Atom Count: 19,117 
  • Modeled Residue Count: 2,601 
  • Deposited Residue Count: 2,745 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicotinate-nucleotide pyrophosphorylase [carboxylating]
A, B, C, D, E
A, B, C, D, E, F, G, H, I
305Homo sapiensMutation(s): 0 
Gene Names: HEL-S-90nQPRT
EC: 2.4.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for Q15274 (Homo sapiens)
Explore Q15274 
Go to UniProtKB:  Q15274
PHAROS:  Q15274
GTEx:  ENSG00000103485 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15274
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NTM

Query on NTM



Download:Ideal Coordinates CCD File
J [auth A]
K [auth B]
L [auth C]
M [auth D]
N [auth E]
J [auth A],
K [auth B],
L [auth C],
M [auth D],
N [auth E],
O [auth F],
P [auth G],
Q [auth H],
R [auth I]
QUINOLINIC ACID
C7 H5 N O4
GJAWHXHKYYXBSV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free:  0.239 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.245α = 90
b = 174.245β = 90
c = 211.684γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Derived calculations, Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description