6U4O | pdb_00006u4o

Crystal structure of recombinant class II fumarase from Schistosoma mansoni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.227 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Characterization of class II fumarase from Schistosoma mansoni provides the molecular basis for selective inhibition.

Cardoso, I.A.de Souza, A.K.L.Burgess, A.M.G.Chalmers, I.W.Hoffmann, K.F.Nonato, M.C.

(2021) Int J Biol Macromol 175: 406-421

  • DOI: https://doi.org/10.1016/j.ijbiomac.2021.01.180
  • Primary Citation Related Structures: 
    6U4O

  • PubMed Abstract: 

    Schistosomiasis is a neglected tropical disease that affects more than 250 million people worldwide. The only drug available for its treatment undergoes first-pass hepatic metabolism and is not capable of preventing reinfection, which makes the search of new therapies urgently needed. Due to the essential role of fumarases in metabolism, these enzymes represent potential targets for developing novel schistosomiasis treatments. Here, we evaluate the expression profiles for class I and class II fumarases from Schistosoma mansoni (SmFH I and SmFH II , respectively), and report the complete characterization of SmFH II . The first SmFH II structure in complex with L-malate was determined at 1.85 Å resolution. The significant thermoshift observed for SmFH II in the presence of identified ligands makes the differential scanning fluorimetry an adequate technique for ligand screening. A complete kinetic characterization of SmFH II was performed, and comparison with the human fumarase (HsFH) revealed differences regarding the turnover number (k cat ). Structural characterization allowed us to identify differences between SmFH II and HsFH that could be explored to design new selective inhibitors. This work represents the very first step towards validate the fumarases as drug targets to treat schistosomiasis. Our results provide the structural basis to rational search for selective ligands.


  • Organizational Affiliation
    • Laboratório de Cristalografia de Proteínas, Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.

Macromolecule Content 

  • Total Structure Weight: 216.48 kDa 
  • Atom Count: 15,372 
  • Modeled Residue Count: 1,912 
  • Deposited Residue Count: 1,952 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fumarate hydrataseA [auth C],
B [auth A],
C [auth D],
D [auth B]
488Schistosoma mansoniMutation(s): 0 
Gene Names: Smp_158240
EC: 4.2.1.2
UniProt
Find proteins for A0A3Q0KQY7 (Schistosoma mansoni)
Explore A0A3Q0KQY7 
Go to UniProtKB:  A0A3Q0KQY7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q0KQY7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMR
(Subject of Investigation/LOI)

Query on LMR



Download:Ideal Coordinates CCD File
E [auth C],
H [auth A],
L [auth D],
N [auth B]
(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth C],
I [auth A],
J [auth A],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth C],
K [auth A],
M [auth D],
P [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.65α = 90
b = 67.86β = 118.61
c = 187.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil308058/2012-7
Sao Paulo Research Foundation (FAPESP)Brazil2008/08262-6

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description