1Z76

Crystal structure of an acidic phospholipase A2 (BthA-I) from Bothrops jararacussu venom complexed with p-bromophenacyl bromide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report



Literature

Structure of BthA-I complexed with p-bromophenacyl bromide: possible correlations with lack of pharmacological activity.

Magro, A.J.Takeda, A.A.Soares, A.M.Fontes, M.R.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1670-1677

  • DOI: 10.1107/S0907444905029598
  • Primary Citation of Related Structures:  
    1Z76

  • PubMed Abstract: 
  • The crystal structure of an acidic phospholipase A(2) isolated from Bothrops jararacussu venom (BthA-I) chemically modified with p-bromophenacyl bromide (BPB) has been determined at 1.85 Angstroms resolution. The catalytic, platelet-aggregation inhib ...

    The crystal structure of an acidic phospholipase A(2) isolated from Bothrops jararacussu venom (BthA-I) chemically modified with p-bromophenacyl bromide (BPB) has been determined at 1.85 Angstroms resolution. The catalytic, platelet-aggregation inhibition, anticoagulant and hypotensive activities of BthA-I are abolished by ligand binding. Electron-density maps permitted unambiguous identification of inhibitor covalently bound to His48 in the substrate-binding cleft. The BthA-I-BPB complex contains three structural regions that are modified after inhibitor binding: the Ca(2+)-binding loop, beta-wing and C-terminal regions. Comparison of BthA-I-BPB with two other BPB-inhibited PLA(2) structures suggests that in the absence of Na(+) ions at the Ca(2+)-binding loop, this loop and other regions of the PLA(2)s undergo structural changes. The BthA-I-BPB structure reveals a novel oligomeric conformation. This conformation is more energetically and conformationally stable than the native structure and the abolition of pharmacological activities by the ligand may be related to the oligomeric structural changes. A residue of the ;pancreatic' loop (Lys69), which is usually attributed as providing the anticoagulant effect, is in the dimeric interface of BthA-I-BPB, leading to a new hypothesis regarding the abolition of this activity by BPB.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction analysis of an acidic phospholipase A(2) complexed with p-bromophenacyl bromide and alpha-tocopherol inhibitors at 1.9- and 1.45-A resolution
      Takeda, A.A., dos Santos, J.I., Marcussi, S., Silveira, L.B., Soares, A.M., Fontes, M.R.
      (2004) Biochim Biophys Acta 1699: 281
    • Crystal structure of an acidic platelet aggregation inhibitor and hypotensive phospholipase A2 in the monomeric and dimeric states: insights into its oligomeric state
      Magro, A.J., Murakami, M.T., Marcussi, S., Soares, A.M., Arni, R.K., Fontes, M.R.
      (2004) Biochem Biophys Res Commun 323: 24

    Organizational Affiliation

    Departamento de Física e Biofísica, Instituto de Biociências, UNESP, Distrito de Rubião Jr s/n, Botucatu-SP, Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
phospholipase A2AB122Bothrops jararacussuMutation(s): 0 
EC: 3.1.1.4
Find proteins for Q8AXY1 (Bothrops jararacussu)
Explore Q8AXY1 
Go to UniProtKB:  Q8AXY1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBP
Query on PBP

Download CCD File 
A, B
p-Bromophenacyl bromide
C8 H6 Br2 O
FKJSFKCZZIXQIP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.034α = 90
b = 83.226β = 112.7
c = 45.56γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-11-27
    Changes: Advisory, Derived calculations, Non-polymer description, Structure summary