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Zou JX, Chua W, Ser Z, Wang SM, Chiang GSH, Sanmugam K, Tan BY, Sobota RM, Li H. Detection of Bacterial Neutral Ceramidase in Diabetic Foot Ulcers with an Optimized Substrate and Chemoenzymatic Probes. Angew Chem Int Ed Engl 2023; 62:e202307553. [PMID: 37340712 DOI: 10.1002/anie.202307553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 06/22/2023]
Abstract
Ceramidases (CDases) are important in controlling skin barrier integrity by regulating ceramide composition and affording downstream signal molecules. While the functions of epidermal CDases are known, roles of neutral CDases secreted by skin-residing microbes are undefined. Here, we developed a one-step fluorogenic substrate, S-B, for specific detection of bacterial CDase activity and inhibitor screening. We identified a non-hydrolyzable substrate mimic, C6, as the best hit. Based on C6, we designed a photoaffinity probe, JX-1, which efficiently detects bacterial CDases. Using JX-1, we identified endogenous low-abundance PaCDase in a P. aeruginosa monoculture and in a mixed skin bacteria culture. Harnessing both S-B and JX-1, we found that CDase activity positively correlates with the relative abundance of P. aeruginosa and is negatively associated with wound area reduction in clinical diabetic foot ulcer patient samples. Overall, our study demonstrates that bacterial CDases are important regulators of skin ceramides and potentially play a role in wound healing.
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Affiliation(s)
- Jiao Xia Zou
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Wisely Chua
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Zheng Ser
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Shi Mei Wang
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | | | | | | | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Hao Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
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Abstract
Neutral ceramidases are key enzymes of sphingolipid metabolism that hydrolyze the fatty acyl/sphingosine amide linkage of ceramide at neutral pH. In this issue of Structure, Airola et al. (2015) present the first crystal structure of human nCDase and show how complexation with phosphate supports a new catalytic mechanism for Zn-dependent amidases while providing a structurally based explanation for ceramide specificity.
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Affiliation(s)
- Lucy Malinina
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
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Airola MV, Allen WJ, Pulkoski-Gross MJ, Obeid LM, Rizzo RC, Hannun YA. Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase. Structure 2015; 23:1482-1491. [PMID: 26190575 PMCID: PMC4830088 DOI: 10.1016/j.str.2015.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/03/2015] [Accepted: 06/11/2015] [Indexed: 01/07/2023]
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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Affiliation(s)
- Michael V Airola
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Stony Brook Cancer Center, Stony Brook, NY 11794, USA
| | - William J Allen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Lina M Obeid
- 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
| | - Robert C Rizzo
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yusuf A Hannun
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Stony Brook Cancer Center, Stony Brook, NY 11794, USA.
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Inoue T, Okino N, Kakuta Y, Hijikata A, Okano H, Goda HM, 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 2009; 284:9566-77. [PMID: 19088069 PMCID: PMC2666609 DOI: 10.1074/jbc.m808232200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 12/08/2008] [Indexed: 11/06/2022] Open
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.
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Affiliation(s)
- Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan.
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