6AL3

Lys49 PLA2 BPII derived from the venom of Protobothrops flavoviridis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

SDS-induced oligomerization of Lys49-phospholipase A2from snake venom.

Matsui, T.Kamata, S.Ishii, K.Maruno, T.Ghanem, N.Uchiyama, S.Kato, K.Suzuki, A.Oda-Ueda, N.Ogawa, T.Tanaka, Y.

(2019) Sci Rep 9: 2330-2330

  • DOI: 10.1038/s41598-019-38861-8

  • PubMed Abstract: 
  • Phospholipase A <sub>2 </sub> (PLA <sub>2 </sub>) is one of the representative toxic components of snake venom. PLA <sub>2 </sub>s are categorized into several subgroups according to the amino acid at position 49, which comprises either Asp49, Lys49, ...

    Phospholipase A 2 (PLA 2 ) is one of the representative toxic components of snake venom. PLA 2 s are categorized into several subgroups according to the amino acid at position 49, which comprises either Asp49, Lys49, Arg49 or Ser49. Previous studies suggested that the Lys49-PLA 2 assembles into an extremely stable dimer. Although the behavior on Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) under reducing or non-reducing conditions suggested the presence of intermolecular disulfide bonds, these bonds were not observed in the crystal structure of Lys49-PLA 2 . The reason for this discrepancy between the crystal structure and SDS-PAGE of Lys49-PLA 2 remains unknown. In this study, we analyzed a Lys49-PLA 2 homologue from Protobothrops flavoviridis (PflLys49-PLA 2 BPII), by biophysical analyses including X-ray crystallography, SDS-PAGE, native-mass spectrometry, and analytical ultracentrifugation. The results demonstrated that PflLys49-PLA 2 BPII spontaneously oligomerized in the presence of SDS, which is one of the strongest protein denaturants.


    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto, 860-0082, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Japan Science and Technology Agency, PRESTO, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan. yoshikazu.tanaka@tohoku.ac.jp.,Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan. yoshikazu.tanaka@tohoku.ac.jp.,Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Basic phospholipase A2 BP-II
A, B, C, D
122Protobothrops flavoviridisMutation(s): 0 
EC: 3.1.1.4
Find proteins for P0DJJ9 (Protobothrops flavoviridis)
Go to UniProtKB:  P0DJJ9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 126.900α = 90.00
b = 126.900β = 90.00
c = 64.880γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Database references