2WPG

Sucrose Hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Apo Structure of Sucrose Hydrolase from Xanthomonas Campestris Pv. Campestris Shows an Open Active-Site Groove

Champion, E.Remaud-Simeon, M.Skov, L.K.Kastrup, J.S.Gajhede, M.Mirza, O.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1309

  • DOI: https://doi.org/10.1107/S0907444909040311
  • Primary Citation of Related Structures:  
    2WPG

  • PubMed Abstract: 

    Glycoside hydrolase family 13 (GH-13) mainly contains starch-degrading or starch-modifying enzymes. Sucrose hydrolases utilize sucrose instead of amylose as the primary glucosyl donor. Here, the catalytic properties and X-ray structure of sucrose hydrolase from Xanthomonas campestris pv. campestris are reported. Sucrose hydrolysis catalyzed by the enzyme follows Michaelis-Menten kinetics, with a K(m) of 60.7 mM and a k(cat) of 21.7 s(-1). The structure of the enzyme was solved at a resolution of 1.9 A in the resting state with an empty active site. This represents the first apo structure from subfamily 4 of GH-13. Comparisons with structures of the highly similar sucrose hydrolase from X. axonopodis pv. glycines most notably showed that residues Arg516 and Asp138, which form a salt bridge in the X. axonopodis sucrose complex and define part of the subsite -1 glucosyl-binding determinants, are not engaged in salt-bridge formation in the resting X. campestris enzyme. In the absence of the salt bridge an opening is created which gives access to subsite -1 from the ;nonreducing' end. Binding of the glucosyl moiety in subsite -1 is therefore likely to induce changes in the conformation of the active-site cleft of the X. campestris enzyme. These changes lead to salt-bridge formation that shortens the groove. Additionally, this finding has implications for understanding the molecular mechanism of the closely related subfamily 4 glucosyl transferase amylosucrase, as it indicates that sucrose could enter the active site from the ;nonreducing' end during the glucan-elongation cycle.


  • Organizational Affiliation

    Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMYLOSUCRASE OR ALPHA AMYLASE637Xanthomonas campestris pv. campestrisMutation(s): 0 
UniProt
Find proteins for Q8P5I2 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25))
Explore Q8P5I2 
Go to UniProtKB:  Q8P5I2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8P5I2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.634α = 90
b = 47.658β = 98.35
c = 87.932γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Database references, Derived calculations, Non-polymer description, Refinement description, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description