PDBsum entry 1k9d

Hydrolase

PDB id: 1k9d

Contents

Protein chain

670 a.a. *

Ligands

GOL ×13

Waters ×650

* Residue conservation analysis

PDB id:

1k9d

Name:

Hydrolase

Title:

The 1.7 a crystal structure of alpha-d-glucuronidase, a family-67 glycoside hydrolase from bacillus stearothermophilus t-1

Structure:

Alpha-d-glucuronidase. Chain: a. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Strain: t1. Gene: agua. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.70Å R-factor: 0.176 R-free: 0.203

Authors:

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

Key ref:

G.Golan et al. (2004). Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications. J Biol Chem, 279, 3014-3024. PubMed id: 14573597 DOI: 10.1074/jbc.M310098200

Date:

29-Oct-01 Release date: 29-Oct-02

Protein chain

Q8VVD2  (Q8VVD2_GEOSE) -  Xylan alpha-1,2-glucuronidase from Geobacillus stearothermophilus

Seq: 679 a.a.

Struc: 670 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.131 - xylan alpha-1,2-glucuronosidase.
• Reaction: Hydrolysis of alpha-D-1,2-(4-O-methyl)glucuronosyl links in the main chain of hardwood xylans.

DOI no: 10.1074/jbc.M310098200

J Biol Chem 279:3014-3024 (2004)

PubMed id: 14573597

Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications.

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

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.

Selected figure(s)

Figure 3.
FIG. 3. The dimeric structure of AguA. a, two views of the suggested AguA dimer, related by a 90° rotation. One of the monomers is shown in blue/green colors, and the other is shown in yellow/red colors. The aldotetraouronic substrate is superimposed here (stick model) to indicate the position of the active site of each monomer. b, an enlarged view of the dimerization contact region, showing the specific interactions between the two monomers (dotted lines).

Figure 5.
FIG. 5. The active site architecture of AguA. a, stereo view of the E285N-substrate complex (red) superimposed with the WT-products complex (green), showing the hydrogen bonds (dotted lines) and distances between the catalytic residues, the nucleophilic water and the substrate/products. The inset on the right shows the two different conformations of the MeGlcA sugar ring in the two complexes. b, a superposition of the E386Q mutant active site (purple), the active site of the WT AguA in complex with the reaction products MeGlcA and xylotriose (green), and the free WT enzyme (cyan), demonstrating the conformational flexibility and movement of the 283-287 loop following substrate binding and catalysis. The relevant parts of WT AguA confirm that it is practically identical to the E386Q mutant.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 3014-3024) copyright 2004.

Figures were selected by an automated process.