Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 115.26 kDa 
• Atom Count: 7656 
• Modelled Residue Count: 1001 
• Deposited Residue Count: 1076 
• Unique protein chains: 1

4YUB

Crystal structure of human Nicotinic Acid Phosphoribosyltransferase

• PDB DOI: 10.2210/pdb4YUB/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-18 Released: 2015-05-20 
• Deposition Author(s): Garavaglia, S., Rizzi, M., Marletta, A.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Crystal structure of human nicotinic acid phosphoribosyltransferase.

Marletta, A.S., Massarotti, A., Orsomando, G., Magni, G., Rizzi, M., Garavaglia, S.

(2015) FEBS Open Bio 5: 419-428

• PubMed: 26042198 
• DOI: 10.1016/j.fob.2015.05.002
• Primary Citation of Related Structures:  
  4YUB


• PubMed Abstract: 
  

Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss-Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent.

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Organizational Affiliation: 

Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate phosphoribosyltransferase	A, B	538	Homo sapiens	Mutation(s): 0  Gene Names: NAPRT, FHIP, NAPRT1 EC: 6.3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q6XQN6 (Homo sapiens) Explore Q6XQN6  Go to UniProtKB:  Q6XQN6
PHAROS:  Q6XQN6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.018	α = 90
b = 101.091	β = 90
c = 125.144	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MR-Rosetta	phasing
SCALA	data scaling
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-18 
• Released Date: 2015-05-20 
Deposition Author(s): Garavaglia, S., Rizzi, M., Marletta, A.S.

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2015-05-27
  Changes: Database references
• Version 1.2: 2015-06-17
  Changes: Database references