1EH5

CRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1 COMPLEXED WITH PALMITATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

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

  • DOI: 10.1073/pnas.080508097
  • Primary Citation of Related Structures:  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 ac ...

    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.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PALMITOYL PROTEIN THIOESTERASE 1
A
279Bos taurusGene Names: PPT1 (PPT)
EC: 3.1.2.22
Find proteins for P45478 (Bos taurus)
Go to Gene View: PPT1
Go to UniProtKB:  P45478
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.520α = 90.00
b = 67.520β = 90.00
c = 128.920γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
TRUNCATEdata reduction
SCALAdata scaling
CNSrefinement
CNSphasing
CCP4data scaling
TRUNCATEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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, Experimental preparation