1GMZ

Crystal structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure of the D49 Phospholipase A2 Piratoxin III from Bothrops Pirajai Reveals Unprecedented Structural Displacement of the Calcium-Binding Loop: Possible Relationship to Cooperative Substrate Binding

Rigden, D.J.Hwa, L.Marangoni, S.Toyama, M.Polikarpov, I.

(2003) Acta Crystallogr.,Sect.D 59: 255


  • PubMed Abstract: 
  • Snake venoms are rich sources of phospholipase A(2) homologues, both active calcium-binding Asp49 enzymes and essentially inactive Lys49 proteins. They are responsible for multiple pharmacological effects, some of which are dependent on catalytic act ...

    Snake venoms are rich sources of phospholipase A(2) homologues, both active calcium-binding Asp49 enzymes and essentially inactive Lys49 proteins. They are responsible for multiple pharmacological effects, some of which are dependent on catalytic activity and others of which are not. Here, the 2.4 A X-ray crystal structure of an active Asp49 phospholipase A(2) from the venom of the snake Bothrops pirajai, refined to conventional and free R values of 20.1 and 25.5%, respectively, is reported. Unusually for phospholipases A(2), the dependence of the enzyme rate on the substrate concentration is sigmoidal, implying cooperativity of substrate binding. The unprecedented structural distortion seen for the calcium-binding loop in the present structure may therefore be indicative of a T-state enzyme. An explanation of the interaction between the substrate-binding sites based on the canonical phospholipase A(2) dimer is difficult. However, an alternative putative dimer interface identified in the crystal lattice brings together the calcium-binding loops of neighbouring molecules, along with the C-terminal regions which are disulfide bonded to those loops, thereby offering a possible route of communication between active sites.


    Organizational Affiliation

    Embrapa Recursos Genéticos e Biotecnologia, Cenargen/Embrapa, Brasília, DF, Brazil. daniel@cenargen.embrapa.br




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A, B
122Bothrops pirajaiEC: 3.1.1.4
Find proteins for P58464 (Bothrops pirajai)
Go to UniProtKB:  P58464
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.019α = 90.00
b = 100.937β = 123.76
c = 48.333γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance