1EXW

CRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1 COMPLEXED WITH HEXADECYLSULFONYL FLUORIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 

Literature

Structural basis for the insensitivity of a serine enzyme (palmitoyl-protein thioesterase) to phenylmethylsulfonyl fluoride.

Das, A.K., Bellizzi III, J.J., Tandel, S., Biehl, E., Clardy, J., Hofmann, S.L.

(2000) J.Biol.Chem. 275: 23847-23851

  • DOI: 10.1074/jbc.M002758200

  • PubMed Abstract: 

    • Palmitoyl-protein thioesterase-1 (PPT1) is a newly described lysosomal enzyme that hydrolyzes long chain fatty acids from lipid-modified cysteine residues in proteins. Deficiency in this enzyme results in a severe neurodegenerative storage disorder, ...

    Palmitoyl-protein thioesterase-1 (PPT1) is a newly described lysosomal enzyme that hydrolyzes long chain fatty acids from lipid-modified cysteine residues in proteins. Deficiency in this enzyme results in a severe neurodegenerative storage disorder, infantile neuronal ceroid lipofuscinosis. Although the primary structure of PPT1 contains a serine lipase consensus sequence, the enzyme is insensitive to commonly used serine-modifying reagents phenylmethylsulfonyl fluoride (PMSF) and diisopropylfluorophosphate. In the current paper, we show that the active site serine in PPT1 is modified by a substrate analog of PMSF, hexadecylsulfonylfluoride (HDSF) in a specific and site-directed manner. The apparent K(i) of the inhibition was 125 micrometer (in the presence of 1.5 mm Triton X-100), and the catalytic rate constant for sulfonylation (k(2)) was 3.3/min, a value similar to previously described sulfonylation reactions. PPT1 was crystallized after inactivation with HDSF, and the structure of the inactive form was determined to 2.4 A resolution. The hexadecylsulfonyl was found to modify serine 115 and to snake through a narrow hydrophobic channel that would not accommodate an aromatic sulfonyl fluoride. Therefore, the geometry of the active site accounts for the reactivity of PPT1 with HDSF but not PMSF. These observations suggest a structural explanation as to why certain serine lipases are resistant to modification by commonly used serine-modifying reagents.

    Organizational Affiliation: 

    Department of Internal Medicine and the Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8593, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PALMITOYL PROTEIN THIOESTERASE 1
A
279Bos taurusMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HDS
Query on HDS
Download SDF File 
Download CCD File 
A
1-HEXADECANOSULFONIC ACID
C16 H34 O3 S
SSILHZFTFWOUJR-UHFFFAOYSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HSFKi: 125000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.243 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.060α = 90.00
b = 69.060β = 90.00
c = 128.030γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
TRUNCATEdata scaling
MOSFLMdata reduction
TRUNCATEdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-02
    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