5CG0

Crystal structure of Spodoptera frugiperda Beta-glycosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Using the Amino Acid Network to Modulate the Hydrolytic Activity of beta-Glycosidases.

Tamaki, F.K.Souza, D.P.Souza, V.P.Ikegami, C.M.Farah, C.S.Marana, S.R.

(2016) PLoS ONE 11: e0167978-e0167978

  • DOI: 10.1371/journal.pone.0167978

  • PubMed Abstract: 
  • The active site residues in GH1 β-glycosidases are compartmentalized into 3 functional regions, involved in catalysis or binding of glycone and aglycone motifs from substrate. However, it still remains unclear how residues outside the active site mod ...

    The active site residues in GH1 β-glycosidases are compartmentalized into 3 functional regions, involved in catalysis or binding of glycone and aglycone motifs from substrate. However, it still remains unclear how residues outside the active site modulate the enzymatic activity. To tackle this question, we solved the crystal structure of the GH1 β-glycosidase from Spodoptera frugiperda (Sfβgly) to systematically map its residue contact network and correlate effects of mutations within and outside the active site. External mutations neighbouring the functional residues involved in catalysis and glycone-binding are deleterious, whereas mutations neighbouring the aglycone-binding site are less detrimental or even beneficial. The large dataset of new and previously characterized Sfβgly mutants supports that external perturbations are coherently transmitted to active site residues possibly through contacts and specifically disturb functional regions they interact to, reproducing the effects observed for direct mutations of functional residues. This allowed us to suggest that positions related to the aglycone-binding site are preferential targets for introduction of mutations aiming to further improve the hydrolytic activity of β-glycosidases.


    Organizational Affiliation

    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-glucosidase
A, B, C, D, E, F
489Spodoptera frugiperdaMutation(s): 2 
Find proteins for O61594 (Spodoptera frugiperda)
Go to UniProtKB:  O61594
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B, C, D, E, F
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.192 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 53.825α = 93.16
b = 64.994β = 92.04
c = 257.189γ = 112.18
Software Package:
Software NamePurpose
HKL-2000data scaling
Cootmodel building
REFMACrefinement
d*TREKdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FAPESPBrazil08/55914-9
FAPESPBrazil14/19439-5
CNPqBrazil08/57908-1
Instituto Nacional de Ciencias e Tecnologia para o BioetanolBrazil574002/2008-1

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Database references, Derived calculations, Refinement description