6KQU

Crystal structure of phospholipase A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Residue Asn21 acts as a switch for calcium binding to modulate the enzymatic activity of human phospholipase A2 group IIE.

Hou, S.Zhang, Y.Xu, J.Bai, J.Liu, J.Xie, J.Xu, T.

(2020) Biochimie 176: 117-121

  • DOI: https://doi.org/10.1016/j.biochi.2020.07.003
  • Primary Citation of Related Structures:  
    6KQU

  • PubMed Abstract: 

    Secreted phospholipases A2 (sPLA2) group IIE (GIIE) is involved in several biological events, such as lipid metabolism and possibly inflammation that may mainly depend on its catalytic reaction. We previously showed that Asn21 is a critical residue that contributes to the enzymatic activity of hGIIE, but the underlying mechanism is still not clear. Here, combined with crystal structures and mutagenesis studies of the Asn21Gly mutant, we demonstrate that Asn21 acts as a switch responsible for the calcium binding and the catalytic efficiency. Our results of the atypical feature of calcium binding in hGIIE not only provide clues to understand the molecular basis of its enzymatic activity and physiological function, but also confer improved specificity for potential inhibitor design of sPLA2.


  • Organizational Affiliation

    State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Group IIE secretory phospholipase A2123Homo sapiensMutation(s): 1 
Gene Names: PLA2G2E
EC: 3.1.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZK7 (Homo sapiens)
Explore Q9NZK7 
Go to UniProtKB:  Q9NZK7
PHAROS:  Q9NZK7
GTEx:  ENSG00000188784 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZK7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download Ideal Coordinates CCD File 
L [auth A]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
K [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.839α = 90
b = 61.117β = 90
c = 63.404γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description