Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 88.77 kDa 
• Atom Count: 6634 
• Modelled Residue Count: 754 
• Deposited Residue Count: 754 
• Unique protein chains: 1

1K8Q

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

• PDB DOI: 10.2210/pdb1K8Q/pdb

• Classification: HYDROLASE
• Organism(s): Canis lupus familiaris
• Expression System: Zea mays
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2001-10-25 Released: 2002-03-06 
• Deposition Author(s): Roussel, A., Miled, N., Berti-Dupuis, L., Riviere, M., Spinelli, S., Berna, P., Gruber, V., Verger, R., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.257 
• R-Value Work: 0.197 

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

• PubMed: 11689574 
• DOI: 10.1074/jbc.M109484200
• Primary Citation of Related Structures:  
  1K8Q


• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triacylglycerol lipase, gastric	A, B	377	Canis lupus familiaris	Mutation(s): 0  Gene Names: LIPF EC: 3.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for P80035 (Canis lupus familiaris) Explore P80035  Go to UniProtKB:  P80035

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	G [auth A], M [auth B]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
C11	H [auth A], N [auth B]	UNDECYL-PHOSPHINIC ACID BUTYL ESTER C15 H33 O2 P QCBLJDSWVGAXQB-UHFFFAOYSA-N
NAG	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.257 
• R-Value Work: 0.197 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.209	α = 90
b = 164.498	β = 90
c = 177.156	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-10-25 
• Released Date: 2002-03-06 
Deposition Author(s): Roussel, A., Miled, N., Berti-Dupuis, L., Riviere, M., Spinelli, S., Berna, P., Gruber, V., Verger, R., Cambillau, C.

Revision History  

• Version 1.0: 2002-03-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary