1G2X

Sequence induced trimerization of krait PLA2: crystal structure of the trimeric form of krait PLA2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Sequence-induced trimerization of phospholipase A2: structure of a trimeric isoform of PLA2 from common krait (Bungarus caeruleus) at 2.5 A resolution.

Singh, G.Gourinath, S.Saravanan, K.Sharma, S.Bhanumathi, S.Betzel, C.h.Srinivasan, A.Singh, T.P.

(2005) Acta Crystallogr.,Sect.F 61: 8-13

  • DOI: 10.1107/S1744309104025503
  • Also Cited By: 2OSN

  • PubMed Abstract: 
  • The venom of the common Indian krait (Bungarus caeruleus) contains about a dozen isoforms of phospholipase A2 (PLA2), which exist in different oligomeric forms as well as in complexes with low-molecular-weight ligands. The basic objective of multimer ...

    The venom of the common Indian krait (Bungarus caeruleus) contains about a dozen isoforms of phospholipase A2 (PLA2), which exist in different oligomeric forms as well as in complexes with low-molecular-weight ligands. The basic objective of multimerization and complexation is either to inactivate PLA2 in the venom for long-term storage, to generate a new PLA2 function or to make a more lethal assembly. The current isoform was isolated from the venom of B. caeruleus. Dynamic light-scattering studies indicated the presence of a stable trimeric association of this PLA2. Its primary sequence was determined by cDNA cloning. The purified protein was crystallized with 2.8 M NaCl as a precipitating agent using the sitting-drop vapour-diffusion method. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 80.9, b = 80.5, c = 57.1 A, beta = 90.3 degrees. The structure was refined to a final R factor of 0.198. This is a novel trimeric PLA2 structure in which the central pore formed by the association of three molecules is filled with water molecules. The interactions across the pore take place via multiple water bridges primarily to the side chains of Arg, Lys and Thr residues. Approximately 12% of the total solvent-accessible surface area is buried in the core of the trimer. The active sites of all three molecules are located on the surface and are fully exposed to the solvent, resulting in a highly potent enzymatic unit.


    Related Citations: 
    • Specific mutations in Krait PLA2 lead to dimerization of protein molecules: Crystal structure of Krait PLA2 at 2.1 resolution.
      Gourinath, S.,Singh, G.,Sharma, S.,Bhanumathi, S.,Betzel, C.,Paramsivam, M.,Srinivasan, A.,Singh, T.P.
      () TO BE PUBLISHED --: --
    • Three-dimensional structure of a novel phospholipase A2 from Indian common krait at 2.45 resolution.
      Singh, G.,Gourinath, S.,Sharma, S.,Paramasivam, M.,Srinivasan, A.,Singh, T.P.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A, B, C
118Bungarus caeruleusMutation(s): 0 
EC: 3.1.1.4
Find proteins for Q6SLM0 (Bungarus caeruleus)
Go to UniProtKB:  Q6SLM0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 80.949α = 90.00
b = 80.572β = 90.35
c = 57.098γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description