6R99 | pdb_00006r99

Crystal Structure of Human CLN protein 5 (Ceroid Lipofuscinosis Neuronal Protein 5)

• PDB DOI: https://doi.org/10.2210/pdb6R99/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-04-03 Released: 2020-04-22 
• Deposition Author(s): Luebben, A.V., Sheldrick, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

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

Luebben, A.V., Bender, D., Becker, S., Crowther, L.M., Erven, I., Hofmann, K., Soding, J., Klemp, H., Bellotti, C., Stauble, A., Qiu, T., Kathayat, R.S., Dickinson, B.C., Gartner, J., Sheldrick, G.M., Kratzner, R., Steinfeld, R.

(2022) Sci Adv 8: eabj8633-eabj8633

• PubMed: 35427157 
• DOI: https://doi.org/10.1126/sciadv.abj8633
• Primary Citation Related Structures: 
  6R99


• PubMed 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.

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Organizational Affiliation: 
• Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany.
Department of Pediatric Neurology, University Children's Hospital Zürich, University of Zurich, Steinwiesstrasse 75, 8032 Zürich, Switzerland.
Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Fassberg 11, 37077 Göttingen, Germany.
Institute for Genetics, University of Cologne, Zülpicher Str.47a, 50674 Cologne, Germany.
Quantitative Biology and Bioinformatics and Department of Molecular Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.
Department of Chemistry, University of Chicago, Chicago, IL, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.36 kDa 
• Atom Count: 2,441 
• Modeled Residue Count: 285 
• Deposited Residue Count: 407 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ceroid-lipofuscinosis neuronal protein 5	A	407	Homo sapiens	Mutation(s): 0  Gene Names: CLN5, hCG_28176
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.42	α = 90
b = 58.42	β = 90
c = 179.05	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Luebben, A.V., Sheldrick, G.M.

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2022-09-28
  Changes: Database references, Structure summary
• Version 2.2: 2024-11-13
  Changes: Data collection, Structure summary