1GMZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • R-Value Observed: 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 D Biol Crystallogr 59: 255

  • DOI: 10.1107/s0907444902021467
  • Primary Citation of Related Structures:  
    1GMZ

  • 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 activity and others of which are not ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOLIPASE A2A, B122Bothrops pirajaiMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for P58464 (Bothrops pirajai)
Explore P58464 
Go to UniProtKB:  P58464
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.019α = 90
b = 100.937β = 123.76
c = 48.333γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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