1HLG

CRYSTAL STRUCTURE OF HUMAN GASTRIC LIPASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.210 

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This is version 2.1 of the entry. See complete history


Literature

Crystal structure of human gastric lipase and model of lysosomal acid lipase, two lipolytic enzymes of medical interest.

Roussel, A.Canaan, S.Egloff, M.P.Riviere, M.Dupuis, L.Verger, R.Cambillau, C.

(1999) J Biol Chem 274: 16995-17002

  • DOI: https://doi.org/10.1074/jbc.274.24.16995
  • Primary Citation of Related Structures:  
    1HLG

  • PubMed Abstract: 

    Fat digestion in humans requires not only the classical pancreatic lipase but also gastric lipase, which is stable and active despite the highly acidic stomach environment. We report here the structure of recombinant human gastric lipase at 3.0-A resolution, the first structure to be described within the mammalian acid lipase family. This globular enzyme (379 residues) consists of a core domain belonging to the alpha/beta hydrolase-fold family and a "cap" domain, which is analogous to that present in serine carboxypeptidases. It possesses a classical catalytic triad (Ser-153, His-353, Asp-324) and an oxyanion hole (NH groups of Gln-154 and Leu-67). Four N-glycosylation sites were identified on the electron density maps. The catalytic serine is deeply buried under a segment consisting of 30 residues, which can be defined as a lid and belonging to the cap domain. The displacement of the lid is necessary for the substrates to have access to Ser-153. A phosphonate inhibitor was positioned in the active site that clearly suggests the location of the hydrophobic substrate binding site. The lysosomal acid lipase was modeled by homology, and possible explanations for some previously reported mutations leading to the cholesterol ester storage disease are given based on the present model.


  • Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, CNRS-IFR1 UPR 9039, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIPASE, GASTRIC
A, B
371Homo sapiensMutation(s): 0 
EC: 3.1.1.3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07098 (Homo sapiens)
Explore P07098 
Go to UniProtKB:  P07098
PHAROS:  P07098
GTEx:  ENSG00000182333 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07098
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P07098-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.210 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 244.33α = 90
b = 244.33β = 90
c = 244.33γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CCP4model building
X-PLORrefinement
CCP4data scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-15
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Structure summary