2OK9

PrTX-I-BPB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a phospholipase A(2) homolog complexed with p-bromophenacyl bromide reveals important structural changes associated with the inhibition of myotoxic activity.

Marchi-Salvador, D.P.Fernandes, C.A.Silveira, L.B.Soares, A.M.Fontes, M.R.

(2009) Biochim.Biophys.Acta 1794: 1583-1590

  • DOI: 10.1016/j.bbapap.2009.07.005

  • PubMed Abstract: 
  • For the first time, the structure of a catalytic inactive phospholipase A(2) homolog (Lys49-PLA(2)s) complexed with p-bromophenacyl bromide (BPB) has been solved by X-ray crystallography. Lys49-PLA(2)s are among the main components of Viperidae snake ...

    For the first time, the structure of a catalytic inactive phospholipase A(2) homolog (Lys49-PLA(2)s) complexed with p-bromophenacyl bromide (BPB) has been solved by X-ray crystallography. Lys49-PLA(2)s are among the main components of Viperidae snake venoms, causing myonecrosis and other actions despite their catalytic inactivity. BPB, a classic inhibitor of catalytic-active PLA(2)s, has been used since the 1970s because it binds specifically the His48 residue of the catalytic site. Curiously, when Lys49-PLA(2) is chemically modified by BPB, it causes a partial inhibition of the myotoxic function which is associated with the C-terminus and not with the catalytic site. The structure of PrTX-I complexed to BPB revealed unambiguously that the inhibitor binds covalently to His48, causing a distortion of the Ca(2)(+)-binding loop region and C-terminus rearrangement in one of its monomers. The comparison between the apo and BPB-complexed PrTX-I structures showed an increased symmetry between the two monomers with the formation of an interchain hydrogen bond between Tyr119 residues. PrTX-I undergoes tertiary and quaternary structural changes when complexed to BPB which could be related to reduction of myotoxicity and other toxic activities. We also proposed a novel myotoxic inhibition hypothesis integrating "myotoxic" and "active" sites for bothropic Lys49-PLA(2)s.


    Organizational Affiliation

    Departamento de Física e Biofísica, Instituto de Biociências, UNESP, Distrito de Rubião Jr., Caixa Postal 510, 18618-000, Botucatu-SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospholipase A2 homolog 1
A, B
121Bothrops pirajaiMutation(s): 0 
Find proteins for P58399 (Bothrops pirajai)
Go to UniProtKB:  P58399
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBP
Query on PBP

Download SDF File 
Download CCD File 
A, B
1-(4-BROMO-PHENYL)-ETHANONE
C8 H7 Br O
WYECURVXVYPVAT-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.602α = 90.00
b = 70.002β = 102.64
c = 43.787γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance