1L8N

The 1.5A crystal structure of alpha-D-glucuronidase from Bacillus stearothermophilus T-1, complexed with 4-O-methyl-glucuronic acid and xylotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report



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

  • 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, ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
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)
Find proteins for Q8VVD2 (Geobacillus stearothermophilus)
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Go to UniProtKB:  Q8VVD2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
B
2 N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCW
Query on GCW

Download CCD File 
A
4-O-methyl-beta-D-glucopyranuronic acid
C7 H12 O7
WGLLPAPKWFDHHV-RLZVPWTLSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.140 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.946α = 90
b = 73.946β = 90
c = 331.341γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary