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 importa ...

    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 IIIAB122Bothrops asperMutation(s): 0 
EC: 3.1.1.4
Find proteins for P20474 (Bothrops asper)
Explore P20474 
Go to UniProtKB:  P20474
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download CCD File 
A, 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 

  • 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