3DKL

Crystal structure of phosphorylated mimic form of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 U S A 106: 13748-13753

  • DOI: 10.1073/pnas.0903898106
  • Primary Citation of Related Structures:  
    3DGR, 3DHD, 3DHF, 3DKJ, 3DKL

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferaseA, B484Homo sapiensMutation(s): 0 
Gene Names: NAMPTPBEFPBEF1
EC: 2.4.2.12
Find proteins for P43490 (Homo sapiens)
Explore P43490 
Go to UniProtKB:  P43490
NIH Common Fund Data Resources
PHAROS  P43490
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRP
Query on PRP

Download CCD File 
B
1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
 Ligand Interaction
UNU
Query on UNU

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A, B
BENZAMIDE
C7 H7 N O
KXDAEFPNCMNJSK-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

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A, B
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.127α = 90
b = 106.589β = 96.78
c = 83.24γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary