2H3D

Crystal Structure of Mouse Nicotinamide Phosphoribosyltransferase/Visfatin/Pre-B Cell Colony Enhancing Factor in Complex with Nicotinamide Mononuleotide

• PDB DOI: https://doi.org/10.2210/pdb2H3D/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-22 Released: 2006-06-20 
• Deposition Author(s): Wang, T., Zhang, X., Bheda, P., Revollo, J.R., Imai, S.I., Wolberger, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Structure of Nampt/PBEF/visfatin, a mammalian NAD(+) biosynthetic enzyme.

Wang, T., Zhang, X., Bheda, P., Revollo, J.R., Imai, S.I., Wolberger, C.

(2006) Nat Struct Mol Biol 13: 661-662

• PubMed: 16783373 
• DOI: https://doi.org/10.1038/nsmb1114
• Primary Citation of Related Structures:  
  2H3B, 2H3D


• PubMed Abstract: 
  

  Nicotinamide phosphoribosyltransferase (Nampt) synthesizes nicotinamide mononucleotide (NMN) from nicotinamide in a mammalian NAD+ biosynthetic pathway and is required for SirT1 activity in vivo. Nampt has also been presumed to be a cytokine (PBEF) or a hormone (visfatin). The crystal structure of Nampt in the presence and absence of NMN shows that Nampt is a dimeric type II phosphoribosyltransferase and provides insights into the enzymatic mechanism.

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Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, Maryland 21205, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 112.47 kDa 
• Atom Count: 7,638 
• Modelled Residue Count: 929 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	494	Mus musculus	Mutation(s): 2  Gene Names: Nampt, Pbef1 EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q99KQ4 (Mus musculus) Explore Q99KQ4  Go to UniProtKB:  Q99KQ4
IMPC:  MGI:1929865

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMN	C [auth A], D [auth B]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.238 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.46	α = 90
b = 107.96	β = 96.98
c = 83.65	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNS	refinement
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-20 
Deposition Author(s): Wang, T., Zhang, X., Bheda, P., Revollo, J.R., Imai, S.I., Wolberger, C.

Revision History  

• Version 1.0: 2006-06-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary