4PKA

Crystal structure of patatin aged with diisopropylphosphorofluoridate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Patatin-17 in Complex with Aged and Non-Aged Organophosphorus Compounds.

Wijeyesakere, S.J.Richardson, R.J.Stuckey, J.A.

(2014) Plos One 9: e108245-e108245

  • DOI: 10.1371/journal.pone.0108245
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Patatin is a non-specific plant lipase and the eponymous member of a broad class of serine hydrolases termed the patatin-like phospholipase domain containing proteins (PNPLAs). Certain PNPLA family members can be inhibited by organophosphorus (OP) co ...

    Patatin is a non-specific plant lipase and the eponymous member of a broad class of serine hydrolases termed the patatin-like phospholipase domain containing proteins (PNPLAs). Certain PNPLA family members can be inhibited by organophosphorus (OP) compounds. Currently, no structural data are available on the modes of interaction between the PNPLAs and OP compounds or their native substrates. To this end, we present the crystal structure of patatin-17 (pat17) in its native state as well as following inhibition with methyl arachidonyl fluorophosphonate (MAFP) and inhibition/aging with diisopropylphosphorofluoridate (DFP). The native pat17 structure revealed the existence of two portals (portal1 and portal2) that lead to its active-site chamber. The DFP-inhibited enzyme underwent the aging process with the negatively charged phosphoryl oxygen, resulting from the loss of an isopropyl group, being within hydrogen-binding distance to the oxyanion hole. The MAFP-inhibited pat17 structure showed that MAFP did not age following its interaction with the nucleophilic serine residue (Ser77) of pat17 since its O-methyl group was intact. The MAFP moiety is oriented with its phosphoryl oxygen in close proximity to the oxyanion hole of pat17 and its O-methyl group located farther away from the oxyanion hole of pat17 relative to the DFP-bound state. The orientation of the alkoxy oxygens within the two OP compounds suggests a role for the oxyanion hole in stabilizing the emerging negative charge on the oxygen during the aging reaction. The arachidonic acid side chain of MAFP could be contained within portals 1 or 2. Comparisons of pat17 in the native, inhibited, and aged states showed no significant global conformational changes with respect to their Cα backbones, consistent with observations from other α/β hydrolases such as group VIIA phospholipase A2.


    Organizational Affiliation

    Toxicology Program, Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, United States of America.,Toxicology Program, Department of Environmental Health Sciences, and Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America.,Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Patatin-17
X
373Solanum cardiophyllumMutation(s): 0 
EC: 3.1.1.-
Find proteins for Q8LPW4 (Solanum cardiophyllum)
Go to UniProtKB:  Q8LPW4
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MIS
Query on MIS
X
L-PEPTIDE LINKINGC6 H14 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.210 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 52.990α = 90.00
b = 52.990β = 90.00
c = 242.780γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
Omodel building
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
AROUnited StatesDAAD19-02-1-0388
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesES07062
University of Michigan Rackham School of Graduate StudiesUnited States--

Revision History 

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy