Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.57 kDa 
• Atom Count: 2319 
• Modelled Residue Count: 279 
• Deposited Residue Count: 279 
• Unique protein chains: 1

1EH5

CRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1 COMPLEXED WITH PALMITATE

• DOI: 10.2210/pdb1EH5/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2000-02-18 Released: 2000-04-26 
• Deposition Author(s): Bellizzi III, J.J., Widom, J., Kemp, C., Lu, J.Y., Das, A.K., Hofmann, S.L., Clardy, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.270 
• R-Value Work: 0.226 
• R-Value Observed: 0.234 

Literature

The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis.

Bellizzi III, J.J., Widom, J., Kemp, C., Lu, J.Y., Das, A.K., Hofmann, S.L., Clardy, J.

(2000) Proc Natl Acad Sci U S A 97: 4573-4578

• PubMed: 10781062 
• DOI: 10.1073/pnas.080508097
• Primary Citation of Related Structures:  
  1EH5, 1EI9


• PubMed Abstract: 
  

Mutations in palmitoyl-protein thioesterase 1 (PPT1), a lysosomal enzyme that removes fatty acyl groups from cysteine residues in modified proteins, cause the fatal inherited neurodegenerative disorder infantile neuronal ceroid lipofuscinosis. The accumulation of undigested substrates leads to the formation of neuronal storage bodies that are associated with the clinical symptoms. Less severe forms of PPT1 deficiency have been found recently that are caused by a distinct set of PPT1 mutations, some of which retain a small amount of thioesterase activity. We have determined the crystal structure of PPT1 with and without bound palmitate by using multiwavelength anomalous diffraction phasing. The structure reveals an alpha/beta-hydrolase fold with a catalytic triad composed of Ser115-His289-Asp233 and provides insights into the structural basis for the phenotypes associated with PPT1 mutations.

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Related Citations: 

• Mutations in the Palmitoyl Protein Thioesterase Gene Causing Infantile Neuronal Ceroid Lipofuscinosis
  Vesa, J., Hellsten, E., Verkruyse, L.A., Camp, L.A., Rapola, J., Santavuori, P., Hofmann, S.L., Peltonen, L.
  (1995) Nature 376: 584

• Purification and Properties of a Palmitoyl Protein Thioesterase that Cleaves Palmitate from H-Ras
  Camp, L.A., Hofmann, S.L.
  (1993) J Biol Chem 268: 22566

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PALMITOYL PROTEIN THIOESTERASE 1	A	279	Bos taurus	Mutation(s): 0  Gene Names: PPT1, CLN1, PPT EC: 3.1.2.22 Membrane Entity: Yes
UniProt
Find proteins for P45478 (Bos taurus) Explore P45478  Go to UniProtKB:  P45478

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM (Subject of Investigation/LOI)	E [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.270 
• R-Value Work: 0.226 
• R-Value Observed: 0.234 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.52	α = 90
b = 67.52	β = 90
c = 128.92	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
TRUNCATE	data reduction
CNS	refinement
CCP4	data scaling
TRUNCATE	data scaling
CNS	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2000-02-18 
• Released Date: 2000-04-26 
Deposition Author(s): Bellizzi III, J.J., Widom, J., Kemp, C., Lu, J.Y., Das, A.K., Hofmann, S.L., Clardy, J.

Revision History  

• Version 1.0: 2000-04-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references
• Version 1.5: 2018-01-31
  Changes: Database references, Experimental preparation
• Version 1.6: 2018-02-28
  Changes: Experimental preparation
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary