PDBsum entry 2vrk

Hydrolase

PDB id: 2vrk

Contents

Protein chains

493 a.a. *

Ligands

PO4 ×4

Waters ×1187

* Residue conservation analysis

PDB id:

2vrk

Name:

Hydrolase

Title:

Structure of a seleno-methionyl derivative of wild type arabinofuranosidase from thermobacillus xylanilyticus

Structure:

Alpha-l-arabinofuranosidase. Chain: a, b, c. Synonym: arabinofuranosidase. Engineered: yes

Source:

Thermobacillus xylanilyticus. Organism_taxid: 76633. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.20Å R-factor: 0.166 R-free: 0.186

Authors:

G.Paes,L.K.Skov,M.J.Odonohue,C.Remond,J.S.Kastrup,M.Gajhede,O.Mirza

Key ref:

G.Paës et al. (2008). The structure of the complex between a branched pentasaccharide and Thermobacillus xylanilyticus GH-51 arabinofuranosidase reveals xylan-binding determinants and induced fit. Biochemistry, 47, 7441-7451. PubMed id: 18563919

Date:

09-Apr-08 Release date: 01-Jul-08

Protein chains

O69262  (O69262_THEXY) -  non-reducing end alpha-L-arabinofuranosidase from Thermobacillus xylanilyticus

Seq: 496 a.a.

Struc: 493 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.55 - non-reducing end alpha-L-arabinofuranosidase.
• Reaction: Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.

Biochemistry 47:7441-7451 (2008)

PubMed id: 18563919

The structure of the complex between a branched pentasaccharide and Thermobacillus xylanilyticus GH-51 arabinofuranosidase reveals xylan-binding determinants and induced fit.

G.Paës, L.K.Skov, M.J.O'Donohue, C.Rémond, J.S.Kastrup, M.Gajhede, O.Mirza.

ABSTRACT

The crystal structure of the family GH-51 alpha- l-arabinofuranosidase from Thermobacillus xylanilyticus has been solved as a seleno-methionyl derivative. In addition, the structure of an inactive mutant Glu176Gln is presented in complex with a branched pentasaccharide, a fragment of its natural substrate xylan. The overall structure shows the two characteristic GH-51 domains: a catalytic domain that is folded into a (beta/alpha) 8-barrel and a C-terminal domain that displays jelly roll architecture. The pentasaccharide is bound in a groove on the surface of the enzyme, with the mono arabinosyl branch entering a tight pocket harboring the catalytic dyad. Detailed analyses of both structures and comparisons with the two previously determined structures from Geobacillus stearothermophilus and Clostridium thermocellum reveal important details unique to the Thermobacillus xylanilyticus enzyme. In the absence of substrate, the enzyme adopts an open conformation. In the substrate-bound form, the long loop connecting beta-strand 2 to alpha-helix 2 closes the active site and interacts with the substrate through residues His98 and Trp99. The results of kinetic and fluorescence titration studies using mutants underline the importance of this loop, and support the notion of an interaction between Trp99 and the bound substrate. We suggest that the changes in loop conformation are an integral part of the T. xylanilyticus alpha- l-arabinofuranosidase reaction mechanism, and ensure efficient binding and release of substrate.