2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of the beta-glucosidase from Bacillus polymyxa

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Structural Basis of Increased Resistance to Thermal Denaturation Induced by Single Amino Acid Substitution in the Sequence of Beta-Glucosidase a from Bacillus Polymyxa.

Sanz-Aparicio, J.Hermoso, J.A.Martinez-Ripoll, M.Gonzalez, B.Lopez-Camacho, C.Polaina, J.

(1998) Proteins 33: 567-576

  • DOI: https://doi.org/10.1002/(sici)1097-0134(19981201)33:4<567::aid-prot9>3.0.co;2-u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The increasing development of the biotechnology industry demands the design of enzymes suitable to be used in conditions that often require broad resistance against adverse conditions. beta-glucosidase A from Bacillus polymyxa is an interesting model for studies of protein engineering. This is a well-characterized enzyme, belonging to glycosyl hydrolase family 1. Its natural substrate is cellobiose, but is also active against various artificial substrates. In its native state has an octameric structure. Its subunit conserves the general (alpha/beta)8 barrel topology of its family, with the active site being in a cavity defined along the axis of the barrel. Using random-mutagenesis, we have identified several mutations enhancing its stability and it was found that one them, the E96K substitution, involved structural changes. The crystal structure of this mutant has been determined by X-ray diffraction and compared with the native structure. The only difference founded between both structures is a new ion pair linking Lys96 introduced at the N-terminus of helix alpha2, to Asp28, located in one of the loops surrounding the active-site cavity. The new ion pair binds two segments of the chain that are distant in sequence and, therefore, this favorable interaction must exert a determinant influence in stabilizing the tertiary structure. Furthermore, analysis of the crystallographic isotropic temperature factors reveals that, as a direct consequence of the introduced ion pair, an unexpected decreased mobility of secondary structure units of the barrel which are proximal to the site of mutation is observed. However, this effect is observed only in the surrounding of one of the partners forming the salt bridge and not around the other. These results show that far-reaching effects can be achieved by a single amino acid replacement within the protein structure. Consequently, the identification and combination of a few single substitutions affecting stability may be sufficient to obtain a highly resistant enzyme, suitable to be used under extreme conditions.

  • Organizational Affiliation

    Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain. xjulia@roca.csic.es

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-GLUCOSIDASE447Paenibacillus polymyxaMutation(s): 1 
Find proteins for P22073 (Paenibacillus polymyxa)
Explore P22073 
Go to UniProtKB:  P22073
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22073
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NFG

Download Ideal Coordinates CCD File 
C [auth A]2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside
C12 H13 F N2 O9
Query on G2F

Download Ideal Coordinates CCD File 
B [auth A]2-deoxy-2-fluoro-alpha-D-glucopyranose
C6 H11 F O5
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.23α = 90
b = 136.23β = 90
c = 173.26γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-05
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references, Structure summary, Version format compliance
  • Version 1.2: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-01
    Changes: Advisory, Derived calculations
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary