1. Academic Validation
  2. Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase

Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase

  • Structure. 2015 Aug 4;23(8):1482-1491. doi: 10.1016/j.str.2015.06.013.
Michael V Airola 1 William J Allen 2 Michael J Pulkoski-Gross 3 Lina M Obeid 4 Robert C Rizzo 2 Yusuf A Hannun 5
Affiliations

Affiliations

  • 1 Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Stony Brook Cancer Center, Stony Brook, NY 11794, USA.
  • 2 Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA.
  • 3 Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
  • 4 Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Stony Brook Cancer Center, Stony Brook, NY 11794, USA; Department of Medicine, Northport Veterans Affairs Medical Center, Northport, NY 11768, USA.
  • 5 Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Stony Brook Cancer Center, Stony Brook, NY 11794, USA. Electronic address: yusuf.hannun@stonybrookmedicine.edu.
Abstract

Neutral Ceramidase (nCDase) catalyzes conversion of the apoptosis-associated lipid ceramide to sphingosine, the precursor for the proliferative factor sphingosine-1-phosphate. As an Enzyme regulating the balance of ceramide and sphingosine-1-phosphate, nCDase is emerging as a therapeutic target for Cancer. Here, we present the 2.6-Å crystal structure of human nCDase in complex with phosphate that reveals a striking, 20-Å deep, hydrophobic active site pocket stabilized by a eukaryotic-specific subdomain not present in Bacterial ceramidases. Utilizing flexible ligand docking, we predict a likely binding mode for ceramide that superimposes closely with the crystallographically observed transition state analog phosphate. Our results suggest that nCDase uses a new catalytic strategy for Zn(2+)-dependent amidases, and generates ceramide specificity by sterically excluding sphingolipids with bulky headgroups and specifically recognizing the small hydroxyl head group of ceramide. Together, these data provide a foundation to aid drug development and establish common themes for how proteins recognize the bioactive lipid ceramide.

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