Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32331.94 
• Atom Count: 2266 
• Residue Count: 279 
• Unique protein chains: 1

1EI9

CRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1

• DOI: 10.2210/pdb1EI9/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Expression System: unidentified baculovirus


• Deposited: 2000-02-24 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: 2.25 Å
• R-Value Free: 0.297 
• R-Value Work: 0.241 

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.USA 97: 4573-4578

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


• 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: 

• Producing Selenomethionine-labeled Proteins with a Baculovirus Expression Vector System
  Bellizzi III, J.J.,Widom, J.,Kemp, C.W.,Clardy, J.
  (1999) Structure 7: R263
• 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

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NDG	A	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.297 
• R-Value Work: 0.241 
• Space Group: P 4₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 69.350	α = 90.00
b = 69.350	β = 90.00
c = 128.390	γ = 90.00

Software Package:

Software Name	Purpose
TRUNCATE	data scaling
MOSFLM	data reduction
SCALA	data scaling
DENZO	data reduction
CNS	refinement
CCP4	data scaling
TRUNCATE	data reduction
SOLVE	phasing
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-02-24 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-04
  Type: Refinement description
• Version 1.4: 2018-01-24
  Type: Database references
• Version 1.5: 2018-01-31
  Type: Database references