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 
  • R-Value Observed: 0.183 

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This is version 1.4 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

  • DOI: 10.1021/bi00009a003
  • Primary Citation of Related Structures:  
    1LPB

  • 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 C11 alkyl phosphonate compound ...

    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: 
    • 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
    • Structure of the Pancreatic Lipase-Procolipase Complex
      Van Tilbeurgh, H., Sarda, L., Verger, R., Cambillau, C.
      (1992) Nature 359: 159

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COLIPASEA95Sus scrofaMutation(s): 0 
Gene Names: CLPS
Membrane Entity: Yes 
UniProt
Find proteins for P02703 (Sus scrofa)
Explore P02703 
Go to UniProtKB:  P02703
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LIPASEB449Homo sapiensMutation(s): 0 
Gene Names: PNLIP
EC: 3.1.1.3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P16233 (Homo sapiens)
Explore P16233 
Go to UniProtKB:  P16233
PHAROS:  P16233
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.7α = 90
b = 133.7β = 90
c = 93.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary