3DKJ

Crystal structure of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT.

Burgos, E.S.Ho, M.C.Almo, S.C.Schramm, V.L.

(2009) Proc.Natl.Acad.Sci.USA 106: 13748-13753

  • DOI: 10.1073/pnas.0903898106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nicotinamide phosphoribosyltransferase (NAMPT) is highly evolved to capture nicotinamide (NAM) and replenish the nicotinamide adenine dinucleotide (NAD(+)) pool during ADP-ribosylation and transferase reactions. ATP-phosphorylation of an active-site ...

    Nicotinamide phosphoribosyltransferase (NAMPT) is highly evolved to capture nicotinamide (NAM) and replenish the nicotinamide adenine dinucleotide (NAD(+)) pool during ADP-ribosylation and transferase reactions. ATP-phosphorylation of an active-site histidine causes catalytic activation, increasing NAM affinity by 160,000. Crystal structures of NAMPT with catalytic site ligands identify the phosphorylation site, establish its role in catalysis, demonstrate unique overlapping ATP and phosphoribosyltransferase sites, and establish reaction coordinate motion. NAMPT structures with beryllium fluoride indicate a covalent H247-BeF(3)(-) as the phosphohistidine mimic. Activation of NAMPT by H247-phosphorylation causes stabilization of the enzyme-phosphoribosylpyrophosphate complex, permitting efficient capture of NAM. Reactant and product structures establish reaction coordinate motion for NAMPT to be migration of the ribosyl anomeric carbon from the pyrophosphate leaving group to the nicotinamide-N1 while the 5-phosphoryl group, the pyrophosphate moiety, and the nicotinamide ring remain fixed in the catalytic site.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide phosphoribosyltransferase
A, B
484Homo sapiensMutation(s): 0 
Gene Names: NAMPT (PBEF, PBEF1)
EC: 2.4.2.12
Find proteins for P43490 (Homo sapiens)
Go to Gene View: NAMPT
Go to UniProtKB:  P43490
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRP
Query on PRP

Download SDF File 
Download CCD File 
A, B
ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
 Ligand Interaction
UNU
Query on UNU

Download SDF File 
Download CCD File 
A, B
BENZAMIDE
C7 H7 N O
KXDAEFPNCMNJSK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PRPKd: 2000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.257α = 90.00
b = 106.811β = 96.72
c = 83.045γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description