Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 113001.88 
• Atom Count: 7478 
• Residue Count: 998 
• Unique protein chains: 1

2E5D

Crystal structure of Human NMPRTase complexed with nicotinamide

• DOI: 10.2210/pdb2E5D/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2006-12-20 Released: 2007-12-25 
• Deposition Author(s): Takahashi, R., Nakamura, S., Kobayashi, Y., Ohkubo, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.209 
• R-Value Work: 0.179 

Literature

Structure and reaction mechanism of human nicotinamide phosphoribosyltransferase

Takahashi, R., Nakamura, S., Nakazawa, T., Minoura, K., Yoshida, T., Nishi, Y., Kobayashi, Y., Ohkubo, T.

(2010) J.Biochem. 147: 95-107

• PubMed: 19819904 
• DOI: 10.1093/jb/mvp152
• Primary Citation of Related Structures:  
  2E5C, 2E5B


• PubMed Abstract: 
  

Nicotinamide (NM) phosphoribosyltransferase (NMPRTase) catalyzes the reaction of NM and 5'-phosphoribosyl-1'-pyrophosphate (PRPP) to form NM mononucleotide (NMN) and pyrophosphate (PPi) in the pathway of NAD-biosynthesis. Monitoring the (1)H and (31)P NMR spectra of the reaction mixture, we found that this reaction is reversible as dictated by the equilibrium constant K = [NMN][PPi]/([NM][PRPP]) = 0.14, which agreed well with the ratio of second-order rate constants for forward and backward reactions, K = 0.16. The crystal structures of this enzyme in the free form and bound to NM and PRPP at the resolution of 2.0-2.2 A were essentially identical to that of the complex with NMN, except for some variations that could facilitate the substitution reaction by fixing the nucleophile and the leaving group for the requisite inversion of configuration at the C1' carbon of the ribose ring. In the active site near the C1' atom of the bound PRPP or NMN, there was neither negatively charged group nor waterproof environment necessary to support the feasibility of a ribo-oxocarbocation intermediate inherent in the S(N)1 mechanism. The structures and catalytic mechanism thus revealed are also discussed in connection with the multiple biological functions of NMPRTase.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Nicotinamide phosphoribosyltransferase	A, B	499	Homo sapiens	Mutation(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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NCA	A, B	NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.209 
• R-Value Work: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.332	α = 90.00
b = 106.227	β = 96.27
c = 82.475	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-12-20 
• Released Date: 2007-12-25 
• Deposition Author(s): Takahashi, R., Nakamura, S., Kobayashi, Y., Ohkubo, T.

Revision History 

• Version 1.0: 2007-12-25
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Derived calculations, Version format compliance