6OB0

Compound 2 bound structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D N82D produced in HEK293-F cells


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of lipoprotein lipase in complex with GPIHBP1.

Arora, R.Nimonkar, A.V.Baird, D.Wang, C.Chiu, C.H.Horton, P.A.Hanrahan, S.Cubbon, R.Weldon, S.Tschantz, W.R.Mueller, S.Brunner, R.Lehr, P.Meier, P.Ottl, J.Voznesensky, A.Pandey, P.Smith, T.M.Stojanovic, A.Flyer, A.Benson, T.E.Romanowski, M.J.Trauger, J.W.

(2019) Proc.Natl.Acad.Sci.USA 116: 10360-10365

  • DOI: 10.1073/pnas.1820171116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lipoprotein lipase (LPL) plays a central role in triglyceride (TG) metabolism. By catalyzing the hydrolysis of TGs present in TG-rich lipoproteins (TRLs), LPL facilitates TG utilization and regulates circulating TG and TRL concentrations. Until very ...

    Lipoprotein lipase (LPL) plays a central role in triglyceride (TG) metabolism. By catalyzing the hydrolysis of TGs present in TG-rich lipoproteins (TRLs), LPL facilitates TG utilization and regulates circulating TG and TRL concentrations. Until very recently, structural information for LPL was limited to homology models, presumably due to the propensity of LPL to unfold and aggregate. By coexpressing LPL with a soluble variant of its accessory protein glycosylphosphatidylinositol-anchored high-density lipoprotein binding protein 1 (GPIHBP1) and with its chaperone protein lipase maturation factor 1 (LMF1), we obtained a stable and homogenous LPL/GPIHBP1 complex that was suitable for structure determination. We report here X-ray crystal structures of human LPL in complex with human GPIHBP1 at 2.5-3.0 Å resolution, including a structure with a novel inhibitor bound to LPL. Binding of the inhibitor resulted in ordering of the LPL lid and lipid-binding regions and thus enabled determination of the first crystal structure of LPL that includes these important regions of the protein. It was assumed for many years that LPL was only active as a homodimer. The structures and additional biochemical data reported here are consistent with a new report that LPL, in complex with GPIHBP1, can be active as a monomeric 1:1 complex. The crystal structures illuminate the structural basis for LPL-mediated TRL lipolysis as well as LPL stabilization and transport by GPIHBP1.


    Organizational Affiliation

    Chemical Biology and Therapeutics, 4002 Basel, Switzerland.,Biotherapeutic and Analytical Technologies, Novartis Institutes for Biomedical Research, Cambridge, MA 02139.,Cardiovascular and Metabolic Disease Area, Novartis Institutes for Biomedical Research, Cambridge, MA 02139.,Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA 02139.,Cardiovascular and Metabolic Disease Area, Novartis Institutes for Biomedical Research, Cambridge, MA 02139; michael.romanowski@novartis.com john.trauger@novartis.com.,Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA 02139.,Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA 02139; michael.romanowski@novartis.com john.trauger@novartis.com.,Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoprotein lipase
A, B, C, D
448Homo sapiensMutation(s): 0 
Gene Names: LPL (LIPD)
EC: 3.1.1.34
Find proteins for P06858 (Homo sapiens)
Go to Gene View: LPL
Go to UniProtKB:  P06858
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
E, F, G, H
131Homo sapiensMutation(s): 2 
Gene Names: GPIHBP1 (HBP1)
Find proteins for Q8IV16 (Homo sapiens)
Go to Gene View: GPIHBP1
Go to UniProtKB:  Q8IV16
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M3D
Query on M3D

Download SDF File 
Download CCD File 
A, B, C, D
7-(3-cyano-4-hydroxyphenyl)-N-[2-(morpholin-4-yl)ethyl]dibenzo[b,f]oxepine-10-carboxamide
C28 H25 N3 O4
WKDYAACRENBHRU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Download SDF File 
Download CCD File 
B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 153.430α = 90.00
b = 191.420β = 90.00
c = 97.180γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
BUSTERrefinement
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-22
    Type: Data collection, Database references
  • Version 1.2: 2019-06-05
    Type: Data collection, Database references