2GVL | pdb_00002gvl

Crystal Structure of Murine NMPRTase

• PDB DOI: https://doi.org/10.2210/pdb2GVL/pdb

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


• Deposited: 2006-05-02 Released: 2006-07-25 
• Deposition Author(s): Khan, J.A., Tao, X., Tong, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.270 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Molecular basis for the inhibition of human NMPRTase, a novel target for anticancer agents.

Khan, J.A., Tao, X., Tong, L.

(2006) Nat Struct Mol Biol 13: 582-588

• PubMed: 16783377 
• DOI: https://doi.org/10.1038/nsmb1105
• Primary Citation Related Structures: 
  2GVG, 2GVJ, 2GVL


• PubMed Abstract: 
  

  Nicotinamide phosphoribosyltransferase (NMPRTase) has a crucial role in the salvage pathway of NAD+ biosynthesis, and a potent inhibitor of NMPRTase, FK866, can reduce cellular NAD+ levels and induce apoptosis in tumors. We have determined the crystal structures at up to 2.1-A resolution of human and murine NMPRTase, alone and in complex with the reaction product nicotinamide mononucleotide or the inhibitor FK866. The structures suggest that Asp219 is a determinant of substrate specificity of NMPRTase, which is confirmed by our mutagenesis studies. FK866 is bound in a tunnel at the interface of the NMPRTase dimer, and mutations in this binding site can abolish the inhibition by FK866. Contrary to current knowledge, the structures show that FK866 should compete directly with the nicotinamide substrate. Our structural and biochemical studies provide a starting point for the development of new anticancer agents.

---

Organizational Affiliation: 
• Department of Biological Sciences, Columbia University, New York, New York 10027, 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: 111.14 kDa 
• Atom Count: 8,133 
• Modeled Residue Count: 928 
• Deposited Residue Count: 982 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	491	Mus musculus	Mutation(s): 1  Gene Names: Nampt 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

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:  0.270 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.263	α = 90
b = 107.736	β = 96.57
c = 83.287	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-25 
Deposition Author(s): Khan, J.A., Tao, X., Tong, L.

Revision History  

• Version 1.0: 2006-07-25
  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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary