Cln5 represents a new type of cysteine-based S-depalmitoylase linked to neurodegeneration

  • Sci Adv. 2022 Apr 15;8(15):eabj8633. doi: 10.1126/sciadv.abj8633.
Anna V Luebben  1 ,  Daniel Bender  2 ,  Stefan Becker  3 ,  Lisa M Crowther  2 ,  Ilka Erven  4 ,  Kay Hofmann  4 ,  Johannes Söding  5 ,  Henry Klemp  6 ,  Cristina Bellotti  2 ,  Andreas Stäuble  2 ,  Tian Qiu  7 ,  Rahul S Kathayat  7 ,  Bryan C Dickinson  7 ,  Jutta Gärtner  6 ,  George M Sheldrick  1 ,  Ralph Krätzner  6 ,  Robert Steinfeld  2  6
Affiliations
  • 1. Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany.
  • 2. Department of Pediatric Neurology, University Children's Hospital Zürich, University of Zurich, Steinwiesstrasse 75, 8032 Zürich, Switzerland.
  • 3. Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Fassberg 11, 37077 Göttingen, Germany.
  • 4. Institute for Genetics, University of Cologne, Zülpicher Str.47a, 50674 Cologne, Germany.
  • 5. Quantitative Biology and Bioinformatics and Department of Molecular Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
  • 6. Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.
  • 7. Department of Chemistry, University of Chicago, Chicago, IL, USA.
PMID: 35427157 DOI: 10.1126/sciadv.abj8633
Abstract

Genetic CLN5 variants are associated with childhood neurodegeneration and Alzheimer's disease; however, the molecular function of ceroid lipofuscinosis neuronal protein 5 (Cln5) is unknown. We solved the Cln5 crystal structure and identified a region homologous to the catalytic domain of members of the N1pC/P60 superfamily of papain-like Enzymes. However, we observed no protease activity for Cln5; and instead, we discovered that Cln5 and structurally related PPPDE1 and PPPDE2 have efficient cysteine palmitoyl thioesterase (S-depalmitoylation) activity using fluorescent substrates. Mutational analysis revealed that the predicted catalytic residues histidine-166 and cysteine-280 are critical for Cln5 thioesterase activity, uncovering a new cysteine-based catalytic mechanism for S-depalmitoylation Enzymes. Last, we found that Cln5-deficient neuronal progenitor cells showed reduced thioesterase activity, confirming live cell function of Cln5 in setting S-depalmitoylation levels. Our results provide new insight into the function of Cln5, emphasize the importance of S-depalmitoylation in neuronal homeostasis, and disclose a new, unexpected enzymatic function for the N1pC/P60 superfamily of proteins.