2ZXC

Ceramidase complexed with C2

Summary for 2ZXC

• Entry DOI: 10.2210/pdb2zxc/pdb
• Descriptor: Neutral ceramidase, ZINC ION, N-[(1R,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]acetamide, ... (7 entities in total)
• Functional Keywords: beta-prism fold surrounded by six alpha helix, hydrolase, lipid metabolism, secreted
• Biological source: Pseudomonas aeruginosa
• Cellular location: Secreted : Q9I596
• Total number of polymer chains: 2
• Total formula weight: 143097.48

Authors

Okano, H.,Inoue, T.,Okino, N.,Kakuta, Y.,Matsumura, H.,Ito, M. (deposition date: 2008-12-22, release date: 2009-02-03, Last modification date: 2024-10-23)

Primary citation

Inoue, T.,Okino, N.,Kakuta, Y.,Hijikata, A.,Okano, H.,Goda, H.M.,Tani, M.,Sueyoshi, N.,Kambayashi, K.,Matsumura, H.,Kai, Y.,Ito, M.
Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase.
J.Biol.Chem., 284:9566-9577, 2009

PubMed Abstract: Ceramidase (CDase; EC 3.5.1.23) hydrolyzes ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. The crystal structures of neutral CDase from Pseudomonas aeruginosa (PaCD) in the C2-ceramide-bound and -unbound forms were determined at 2.2 and 1.4 A resolutions, respectively. PaCD consists of two domains, and the Zn(2+)- and Mg(2+)/Ca(2+)-binding sites are found within the center of the N-terminal domain and the interface between the domains, respectively. The structural comparison between the C2-ceramide-bound and unbound forms revealed an open-closed conformational change occurring to loop I upon binding of C2-ceramide. In the closed state, this loop sits above the Zn(2+) coordination site and over the opening to the substrate binding site. Mutational analyses of residues surrounding the Zn(2+) of PaCD and rat neutral CDase revealed that the cleavage or creation of the N-acyl linkage of ceramide follows a similar mechanism as observed for the Zn(2+)-dependent carboxypeptidases. The results provide an understanding of the molecular mechanism of hydrolysis and synthesis of ceramide by the enzyme. Furthermore, insights into the actions of PaCD and eukaryotic neutral CDases as an exotoxin and mediators of sphingolipid signaling are also revealed, respectively.

PubMed: 19088069
DOI: 10.1074/jbc.M808232200

Experimental method

X-RAY DIFFRACTION (2.2 Å)