5TFV

Crystal Structure of MT-I isolated from Bothrops asper venom.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a phospholipase A2 from Bothrops asper venom: Insights into a new putative "myotoxic cluster".

Salvador, G.H.Dos Santos, J.I.Lomonte, B.Fontes, M.R.

(2017) Biochimie 133: 95-102

  • DOI: 10.1016/j.biochi.2016.12.015
  • Primary Citation of Related Structures:  
    5TFV

  • PubMed Abstract: 
  • Snake venoms from the Viperidae and Elapidae families often have several phospholipases A 2 (PLA 2 s), which may display different functions despite having a similar structural scaffold. These proteins are considered an important target for the development of drugs against local myotoxic damage because they are not efficiently neutralized by conventional serum therapy ...

    Snake venoms from the Viperidae and Elapidae families often have several phospholipases A 2 (PLA 2 s), which may display different functions despite having a similar structural scaffold. These proteins are considered an important target for the development of drugs against local myotoxic damage because they are not efficiently neutralized by conventional serum therapy. PLA 2 s from these venoms are generally divided into two classes: (i) catalytic PLA 2 s (or Asp49-PLA 2 s) and (ii) non-catalytic PLA 2 -like toxins (or Lys49-PLA 2 s). In many Viperidae venoms, a subset of the basic Asp49-PLA 2 s displays some functional and structural characteristics of PLA 2 -like proteins and group within the same phylogenetic clade, but their myotoxic mechanism is still largely unknown. In the present study, we have crystallized and solved the structure of myotoxin I (MT-I), a basic myotoxic Asp49-PLA 2 isolated from Bothrops asper venom. The structure presents a dimeric conformation that is compatible with that of previous dimers found for basic myotoxic Asp49-PLA 2 s and Lys49-PLA 2 s and has been confirmed by other biophysical and bioinformatics techniques. This arrangement suggests a possible cooperative action between both monomers to exert myotoxicity via two different sites forming a putative membrane-docking site (MDoS) and a putative membrane disruption site (MDiS). This mechanism would resemble that proposed for Lys49-PLA 2 s, but the sites involved appear to be situated in a different region. Thus, as both sites are close to one another, they form a "myotoxic cluster", which is also found in two other basic myotoxic Asp49-PLA 2 s from Viperidae venoms. Such arrangement may represent a novel structural strategy for the mechanism of muscle damage exerted by the group of basic, Asp49-PLA 2 s found in viperid snake venoms.


    Organizational Affiliation

    Departamento de Física e Biofísica, Instituto de Biociências, UNESP - Univ. Estadual Paulista, Botucatu, SP, Brazil. Electronic address: fontes@ibb.unesp.br.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Basic phospholipase A2 myotoxin IIIA, B122Bothrops asperMutation(s): 0 
EC: 3.1.1.4
Membrane Entity: Yes 
UniProt
Find proteins for P20474 (Bothrops asper)
Explore P20474 
Go to UniProtKB:  P20474
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.534α = 90
b = 56.534β = 90
c = 136.459γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil--

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence