Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.36 kDa 
• Atom Count: 6401 
• Residue Count: 671 
• Unique protein chains: 1

1L8N

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

• DOI: 10.2210/pdb1L8N/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-03-21 Released: 2003-03-21 
• Deposition Author(s): Golan, G., Shallom, D., Teplitsky, A., Zaide, G., Shulami, S., Baasov, T., Stojanoff, V., Thompson, A., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

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

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

• PubMed: 14573597 
• 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, 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-D-GLUCURONIDASE	A	679	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: aguA EC: 3.2.1.139 (PDB Primary Data), 3.2.1.131 (UniProt)
Find proteins for Q8VVD2 (Geobacillus stearothermophilus) Explore Q8VVD2  Go to UniProtKB:  Q8VVD2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B	2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCW	A	4-O-methyl-beta-D-glucopyranuronic acid C7 H12 O7 WGLLPAPKWFDHHV-RLZVPWTLSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 73.946	α = 90
b = 73.946	β = 90
c = 331.341	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
SHELXL-97	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-21 
• Released Date: 2003-03-21 
Deposition Author(s): Golan, G., Shallom, D., Teplitsky, A., Zaide, G., Shulami, S., Baasov, T., Stojanoff, V., Thompson, A., Shoham, Y., Shoham, G.

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