1K9D

The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from Bacillus stearothermophilus T-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

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


Literature

Crystal Structures of Geobacillus stearothermophilus {alpha}-Glucuronidase Complexed with Its Substrate and Products: MECHANISTIC IMPLICATIONS.

Golan, G., Shallom, D., Teplitsky, A., Zaide, G., Shulami, S., Baasov, T., Stojanoff, V., Thompson, A., Shoham, Y., Shoham, G.

(2004) J Biol Chem 279: 3014-3024

  • DOI: https://doi.org/10.1074/jbc.M310098200
  • Primary Citation of Related Structures:  
    1K9D, 1K9E, 1K9F, 1L8N, 1MQP, 1MQQ, 1MQR

  • PubMed Abstract: 

    • Alpha-glucuronidases cleave the alpha-1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid and short xylooligomers as part of the hemicellulose degradation system. To date, all of the alpha-glucuronidases are classified as family 67 glycosidases, which catalyze the hydrolysis via the investing mechanism ...

    Alpha-glucuronidases cleave the alpha-1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid and short xylooligomers as part of the hemicellulose degradation system. To date, all of the alpha-glucuronidases are classified as family 67 glycosidases, which catalyze the hydrolysis via the investing mechanism. Here we describe several high resolution crystal structures of the alpha-glucuronidase (AguA) from Geobacillus stearothermophilus, in complex with its substrate and products. In the complex of AguA with the intact substrate, the 4-O-methyl-d-glucuronic acid sugar ring is distorted into a half-chair conformation, which is closer to the planar conformation required for the oxocarbenium ion-like transition state structure. In the active site, a water molecule is coordinated between two carboxylic acids, in an appropriate position to act as a nucleophile. From the structural data it is likely that two carboxylic acids, Asp(364) and Glu(392), activate together the nucleophilic water molecule. The loop carrying the catalytic general acid Glu(285) cannot be resolved in some of the structures but could be visualized in its "open" and "closed" (catalytic) conformations in other structures. The protonated state of Glu(285) is presumably stabilized by its proximity to the negative charge of the substrate, representing a new variation of substrate-assisted catalysis mechanism.

    Organizational Affiliation: 

    Department of Inorganic Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
alpha-D-glucuronidaseA679Geobacillus stearothermophilusMutation(s): 0 
Gene Names: aguA
EC: 3.2.1.139 (PDB Primary Data), 3.2.1.131 (UniProt)
UniProt
Find proteins for Q8VVD2 (Geobacillus stearothermophilus)
Explore Q8VVD2 
Go to UniProtKB:  Q8VVD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VVD2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.57α = 90
b = 73.57β = 90
c = 329.96γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance