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 

Starting Model: experimental
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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

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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