3V8E

Crystal structure of the yeast nicotinamidase Pnc1p bound to the inhibitor nicotinaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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Literature

Structural and Kinetic Isotope Effect Studies of Nicotinamidase (Pnc1) from Saccharomyces cerevisiae.

Smith, B.C.Anderson, M.A.Hoadley, K.A.Keck, J.L.Cleland, W.W.Denu, J.M.

(2012) Biochemistry 51: 243-256

  • DOI: 10.1021/bi2015508
  • Primary Citation of Related Structures:  
    3V8E

  • PubMed Abstract: 
  • Nicotinamidases catalyze the hydrolysis of nicotinamide to nicotinic acid and ammonia. Nicotinamidases are absent in mammals but function in NAD(+) salvage in many bacteria, yeast, plants, protozoa, and metazoans. We have performed structural and kinetic investigations of the nicotinamidase from Saccharomyces cerevisiae (Pnc1) ...

    Nicotinamidases catalyze the hydrolysis of nicotinamide to nicotinic acid and ammonia. Nicotinamidases are absent in mammals but function in NAD(+) salvage in many bacteria, yeast, plants, protozoa, and metazoans. We have performed structural and kinetic investigations of the nicotinamidase from Saccharomyces cerevisiae (Pnc1). Steady-state product inhibitor analysis revealed an irreversible reaction in which ammonia is the first product released, followed by nicotinic acid. A series of nicotinamide analogues acting as inhibitors or substrates were examined, revealing that the nicotinamide carbonyl oxygen and ring nitrogen are critical for binding and reactivity. X-ray structural analysis revealed a covalent adduct between nicotinaldehyde and Cys167 of Pnc1 and coordination of the nicotinamide ring nitrogen to the active-site zinc ion. Using this structure as a guide, the function of several residues was probed via mutagenesis and primary (15)N and (13)C kinetic isotope effects (KIEs) on V/K for amide bond hydrolysis. The KIE values of almost all variants were increased, indicating that C-N bond cleavage is at least partially rate limiting; however, a decreased KIE for D51N was indicative of a stronger commitment to catalysis. In addition, KIE values using slower alternate substrates indicated that C-N bond cleavage is at least partially rate limiting with nicotinamide to highly rate limiting with thionicotinamide. A detailed mechanism involving nucleophilic attack of Cys167, followed by elimination of ammonia and then hydrolysis to liberate nicotinic acid, is discussed. These results will aid in the design of mechanism-based inhibitors to target pathogens that rely on nicotinamidase activity.


    Organizational Affiliation

    Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NicotinamidaseA, B, C, D, E, F, G216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNC1YGL037C
EC: 3.5.1.19
Find proteins for P53184 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53184 
Go to UniProtKB:  P53184
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 298.717α = 90
b = 298.717β = 90
c = 112.652γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-25
    Type: Initial release