1LPB

THE 2.46 ANGSTROMS RESOLUTION STRUCTURE OF THE PANCREATIC LIPASE COLIPASE COMPLEX INHIBITED BY A C11 ALKYL PHOSPHONATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The 2.46 A resolution structure of the pancreatic lipase-colipase complex inhibited by a C11 alkyl phosphonate.

Egloff, M.P.Marguet, F.Buono, G.Verger, R.Cambillau, C.van Tilbeurgh, H.

(1995) Biochemistry 34: 2751-2762


  • PubMed Abstract: 
  • Pancreatic lipase belongs to the serine esterase family and can therefore be inhibited by classical serine reagents such as diisopropyl fluoride or E600. In an attempt to further characterize the active site and catalytic mechanism, we synthesized a ...

    Pancreatic lipase belongs to the serine esterase family and can therefore be inhibited by classical serine reagents such as diisopropyl fluoride or E600. In an attempt to further characterize the active site and catalytic mechanism, we synthesized a C11 alkyl phosphonate compound. This compound is an effective inhibitor of pancreatic lipase. The crystal structure of the pancreatic lipase-colipase complex inhibited by this compound was determined at a resolution of 2.46 A and refined to a final R-factor of 18.3%. As was observed in the case of the structure of the ternary pancreatic lipase-colipase-phospholipid complex, the binding of the ligand induces rearrangements of two surface loops in comparison with the closed structure of the enzyme (van Tilbeurgh et al., 1993b). The inhibitor, which could be clearly observed in the active site, was covalently bound to the active site serine Ser152. A racemic mixture of the inhibitor was used in the crystallization, and there exists evidence that both enantiomers are bound at the active site. The C11 alkyl chain of the first enantiomer fits into a hydrophobic groove and is though to thus mimic the interaction between the leaving fatty acid of a triglyceride substrate and the protein. The alkyl chain of the second enantiomer also has an elongated conformation and interacts with hydrophobic patches on the surface of the open amphipathic lid. This may indicate the location of a second alkyl chain of a triglyceride substrate. Some of the detergent molecules, needed for the crystallization, were also observed in the crystal. Some of them were located at the entrance of the active site, bound to the hydrophobic part of the lid. On the basis of this crystallographic study, a hypothesis about the binding mode of real substrates and the organization of the active site is proposed.


    Related Citations: 
    • Structure of the Pancreatic Lipase-Procolipase Complex
      Van Tilbeurgh, H.,Sarda, L.,Verger, R.,Cambillau, C.
      (1992) Nature 359: 159
    • Interfacial Activation of the Lipase-Procolipase Complex by Mixed Micelles Revealed by X-Ray Crystallography
      Van Tilbeurgh, H.,Egloff, M.-P.,Martinez, C.,Rugani, N.,Verger, R.,Cambillau, C.
      (1993) Nature 362: 814


    Organizational Affiliation

    Laboratoire de Cristallisation et Cristallographie des Macromolécules Biologiques, URA 1296-CNRS, Faculté de Médecine Nord, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COLIPASE
A
95Sus scrofaGene Names: CLPS
Find proteins for P02703 (Sus scrofa)
Go to Gene View: CLPS
Go to UniProtKB:  P02703
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LIPASE
B
449Homo sapiensGene Names: PNLIP
EC: 3.1.1.3
Find proteins for P16233 (Homo sapiens)
Go to Gene View: PNLIP
Go to UniProtKB:  P16233
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MUP
Query on MUP

Download SDF File 
Download CCD File 
B
METHOXYUNDECYLPHOSPHINIC ACID
C12 H27 O3 P
JBVUSHKPEBKWQP-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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: 2.46 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.183 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 133.700α = 90.00
b = 133.700β = 90.00
c = 93.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other