1V02

Crystal structure of the Sorghum bicolor dhurrinase 1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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This is version 1.2 of the entry. See complete history. 


Literature

Structural Determinants of Substrate Specificity in Family 1 Beta-Glucosidases: Novel Insights from the Crystal Structure of Sorghum Dhurrinase-1, a Plant Beta-Glucosidase with Strict Specificity, in Complex with its Natural Substrate

Verdoucq, L., Moriniere, J., Bevan, D.R., Esen, A., Vasella, A., Henrissat, B., Czjzek, M.

(2004) J Biol Chem 279: 31796

  • DOI: https://doi.org/10.1074/jbc.M402918200
  • Primary Citation of Related Structures:  
    1V02, 1V03, 1V08

  • PubMed Abstract: 

    • Plant beta-glucosidases play a crucial role in defense against pests. They cleave, with variable specificity, beta-glucosides to release toxic aglycone moieties. The Sorghum bicolor beta-glucosidase isoenzyme Dhr1 has a strict specificity for its natural substrate dhurrin (p-hydroxy-(S)-mandelonitrile-beta-D-glucoside), whereas its close homolog, the maize beta-glucosidase isoenzyme Glu1, which shares 72% sequence identity, hydrolyzes a broad spectrum of substrates in addition to its natural substrate 2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxaxin-3-one ...

    Plant beta-glucosidases play a crucial role in defense against pests. They cleave, with variable specificity, beta-glucosides to release toxic aglycone moieties. The Sorghum bicolor beta-glucosidase isoenzyme Dhr1 has a strict specificity for its natural substrate dhurrin (p-hydroxy-(S)-mandelonitrile-beta-D-glucoside), whereas its close homolog, the maize beta-glucosidase isoenzyme Glu1, which shares 72% sequence identity, hydrolyzes a broad spectrum of substrates in addition to its natural substrate 2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxaxin-3-one. Structural data from enzyme.substrate complexes of Dhr1 show that the mode of aglycone binding differs from that previously observed in the homologous maize enzyme. Specifically, the data suggest that Asn(259), Phe(261), and Ser(462), located in the aglycone-binding site of S. bicolor Dhr1, are crucial for aglycone recognition and binding. The tight binding of the aglycone moiety of dhurrin promotes the stabilization of the reaction intermediate in which the glycone moiety is in a deformed (1)S(3) conformation within the glycone-binding site, ready for nucleophilic attack to occur. Compared with the broad specificity maize beta-glucosidase, this different binding mode explains the narrow specificity of sorghum dhurrinase-1.

    Organizational Affiliation: 

    Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DHURRINASE
A, B, C, D, F
565Sorghum bicolorMutation(s): 0 
EC: 3.2.1.21
UniProt
Find proteins for Q41290 (Sorghum bicolor)
Explore Q41290 
Go to UniProtKB:  Q41290
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41290
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DHURRINASE565Sorghum bicolorMutation(s): 0 
EC: 3.2.1.21
UniProt
Find proteins for Q41290 (Sorghum bicolor)
Explore Q41290 
Go to UniProtKB:  Q41290
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41290
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.05α = 90
b = 101.05β = 90
c = 279.05γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-20
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance