1K8Q

CRYSTAL STRUCTURE OF DOG GASTRIC LIPASE IN COMPLEX WITH A PHOSPHONATE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the open form of dog gastric lipase in complex with a phosphonate inhibitor.

Roussel, A.Miled, N.Berti-Dupuis, L.Riviere, M.Spinelli, S.Berna, P.Gruber, V.Verger, R.Cambillau, C.

(2002) J.Biol.Chem. 277: 2266-2274

  • DOI: 10.1074/jbc.M109484200

  • PubMed Abstract: 
  • Fat digestion in humans and some mammals such as dogs requires the successive intervention of two lipases: gastric lipase, which is stable and active despite the highly acidic stomach environment, followed by the classical pancreatic lipase secreted ...

    Fat digestion in humans and some mammals such as dogs requires the successive intervention of two lipases: gastric lipase, which is stable and active despite the highly acidic stomach environment, followed by the classical pancreatic lipase secreted into the duodenum. We previously solved the structure of recombinant human gastric lipase (HGL) at 3.0-A resolution in its closed form; this was the first structure to be described within the mammalian acid lipase family. Here we report on the open structure of the recombinant dog gastric lipase (r-DGL) at 2.7-A resolution in complex with the undecyl-butyl (C11Y4) phosphonate inhibitor. HGL and r-DGL show 85.7% amino acid sequence identity, which makes it relevant to compare the forms from two different species. The open r-DGL structure confirms the previous description of the HGL catalytic triad (Ser(153), His(353), and Asp(324)) with the catalytic serine buried and an oxyanion hole (NH groups of Gln(154) and Leu(67)). In r-DGL, the binding of the C11Y4 phosphonate inhibitor induces part of the cap domain, the lid, to roll over the enzyme surface and to expose a catalytic crevice measuring approximately 20 x 20 x 7 A(3). The C11Y4 phosphonate fits into this crevice, and a molecule of beta-octyl glucoside fills up the crevice. The C11Y4 phosphonate inhibitor and the detergent molecule suggest a possible binding mode for the natural substrates, the triglyceride molecules.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 6098, and Laboratoire de Lipolyse Enzymatique, CNRS UPR 9025, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Triacylglycerol lipase, gastric
A, B
377Canis lupus familiarisGene Names: LIPF
EC: 3.1.1.3
Find proteins for P80035 (Canis lupus familiaris)
Go to Gene View: LIPF
Go to UniProtKB:  P80035
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C11
Query on C11

Download SDF File 
Download CCD File 
A, B
UNDECYL-PHOSPHINIC ACID BUTYL ESTER
C15 H33 O2 P
QCBLJDSWVGAXQB-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Download SDF File 
Download CCD File 
A, B
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 61.209α = 90.00
b = 164.498β = 90.00
c = 177.156γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
CCP4data scaling
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-06
    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