Lysosomal Phospholipase A2 in complex with Zinc

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  OPM

  • Deposited: 2018-10-22 Released: 2019-03-20 
  • Deposition Author(s): Bouley, R., Tesmer, J.J.G.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report

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This is version 1.5 of the entry. See complete history


Structural Basis of Lysosomal Phospholipase A2Inhibition by Zn2.

Bouley, R.A.Hinkovska-Galcheva, V.Shayman, J.A.Tesmer, J.J.G.

(2019) Biochemistry 58: 1709-1717

  • DOI: https://doi.org/10.1021/acs.biochem.8b01124
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Lysosomal phospholipase A 2 (LPLA 2 /PLA2G15) is a key enzyme involved in lipid homeostasis and is characterized by both phospholipase A2 and transacylase activity and by an acidic pH optimum. Divalent cations such as Ca 2+ and Mg 2+ have previously been shown to have little effect on the activity of LPLA 2 , but the discovery of a novel crystal form of LPLA 2 with Zn 2+ bound in the active site suggested a role for this divalent cation in regulating enzyme activity. In this complex, the cation directly coordinates the serine and histidine of the α/β-hydrolase triad and stabilizes a closed conformation. This closed conformation is characterized by an inward shift of the lid loop, which extends over the active site and effectively blocks access to one of its lipid acyl chain binding tracks. Therefore, we hypothesized that Zn 2+ would inhibit LPLA 2 activity at a neutral but not acidic pH because histidine would be positively charged at lower pH. Indeed, Zn 2+ was found to inhibit the esterase activity of LPLA 2 in a noncompetitive manner exclusively at a neutral pH (between 6.5 and 8.0). Because lysosomes are reservoirs of Zn 2+ in cells, the pH optimum of LPLA 2 might allow it to catalyze acyl transfer unimpeded within the organelle. We conjecture that Zn 2+ inhibition of LPLA 2 at higher pH maintains a lower activity of the esterase in environments where its activity is not typically required.

  • Organizational Affiliation

    Life Sciences Institute and Department of Pharmacology , University of Michigan , Ann Arbor , Michigan 48109 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Group XV phospholipase A2
A, B
380Homo sapiensMutation(s): 0 
Gene Names: PLA2G15LYPLA3UNQ341/PRO540
EC: 2.3.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NCC3 (Homo sapiens)
Explore Q8NCC3 
Go to UniProtKB:  Q8NCC3
GTEx:  ENSG00000103066 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NCC3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth B],
K [auth B]
C8 H15 N O6
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.567α = 90
b = 84.567β = 90
c = 321.744γ = 120
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL122416

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2020-06-17
    Changes: Data collection, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary