2OXE

Structure of the Human Pancreatic Lipase-related Protein 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation.

Eydoux, C.Spinelli, S.Davis, T.L.Walker, J.R.Seitova, A.Dhe-Paganon, S.De Caro, A.Cambillau, C.Carriere, F.

(2008) Biochemistry 47: 9553-9564

  • DOI: 10.1021/bi8005576
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional con ...

    Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional conformation have required cocrystallization with amphiphiles. Here we report two crystal structures of wild-type and unglycosylated human pancreatic lipase-related protein 2 (HPLRP2) with the lid in an open conformation in the absence of amphiphiles. These structures solved independently are strikingly similar, with some residues of the lid being poorly defined in the electron-density map. The open conformation of the lid is however different from that previously observed in classical liganded PL, suggesting different kinetic properties for HPLRP2. Here we show that the HPLRP2 is directly inhibited by E600, does not present interfacial activation, and acts preferentially on substrates forming monomers or small aggregates (micelles) dispersed in solution like monoglycerides, phospholipids and galactolipids, whereas classical PL displays reverse properties and a high specificity for unsoluble substrates like triglycerides and diglycerides forming oil-in-water interfaces. These biochemical properties imply that the lid of HPLRP2 is likely to spontaneously adopt in solution the open conformation observed in the crystal structure. This open conformation generates a large cavity capable of accommodating the digalactose polar head of galactolipids, similar to that previously observed in the active site of the guinea pig PLRP2, but absent from the classical PL. Most of the structural and kinetic properties of HPLRP2 were found to be different from those of rat PLRP2, the structure of which was previously obtained with the lid in a closed conformation. Our findings illustrate the essential role of the lid in determining the substrate specificity and the mechanism of action of lipases.


    Related Citations: 
    • Two Novel Human Pancreatic Lipase Related Proteins, hPLRP1 and hPLRP2
      Giller, T.,Buchwald, P.,Blum-Kaelin, D.,Hunziker, W.
      (1992) J.Biol.Chem. 267: 16509
    • Human Pancreatic Lipase-Related Protein 2 Is a Galactolipase
      Sias, B.,Ferrato, F.,Grandval, P.,Lafont, D.,Boullanger, P.,De Caro, A.,Leboeuf, B.,Verger, R.,Carriere, F.
      (2004) Biochemistry 43: 10138


    Organizational Affiliation

    CNRS UPR9025 Laboratoire d'Enzymologie Interfaciale et de Physiologie de la Lipolyse, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pancreatic lipase-related protein 2
A, B
466Homo sapiensMutation(s): 0 
Gene Names: PNLIPRP2 (PLRP2)
EC: 3.1.1.26, 3.1.1.3
Find proteins for P54317 (Homo sapiens)
Go to Gene View: PNLIPRP2
Go to UniProtKB:  P54317
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 216.922α = 90.00
b = 216.922β = 90.00
c = 123.618γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance