PDBsum entry: 1uhv

Hydrolase

PDB id: 1uhv

Contents

Protein chains

500 a.a. *

Ligands

DFX ×4

Waters ×1220

* Residue conservation analysis

PDB id:

1uhv

Name:

Hydrolase

Title:

Crystal structure of beta-d-xylosidase from thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase

Structure:

Beta-xylosidase. Chain: a, b, c, d. Synonym: beta-d-xylosiase, 1,4-beta-d-xylan xylohydrolase, xylan 1,4-beta-xylosidase. Engineered: yes

Source:

Thermoanaerobacterium saccharolyticum. Organism_taxid: 28896. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.10Å R-factor: 0.210 R-free: 0.262

Authors:

J.K.Yang,H.J.Yoon,H.J.Ahn,B.Il Lee,J.D.Pedelacq,E.C.Liong, J.Berendzen,M.Laivenieks,C.Vieille,G.J.Zeikus,D.J.Vocadlo, S.G.Withers,S.W.Suh

Key ref:

J.K.Yang et al. (2004). Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase. J Mol Biol, 335, 155-165. PubMed id: 14659747 DOI: 10.1016/j.jmb.2003.10.026

Date:

11-Jul-03 Release date: 23-Dec-03

Protein chains

P36906  (XYNB_THESA) -  Beta-xylosidase

Seq: 500 a.a.

Struc: 500 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.37 - Xylan 1,4-beta-xylosidase.
• Reaction: Hydrolysis of 1,4-beta-D-xylans so as to remove successive D-xylose residues from the non-reducing termini.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (6 terms)

DOI no: 10.1016/j.jmb.2003.10.026

J Mol Biol 335:155-165 (2004)

PubMed id: 14659747

Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase.

J.K.Yang, H.J.Yoon, H.J.Ahn, B.I.Lee, J.D.Pedelacq, E.C.Liong, J.Berendzen, M.Laivenieks, C.Vieille, G.J.Zeikus, D.J.Vocadlo, S.G.Withers, S.W.Suh.

ABSTRACT

1,4-beta-D-Xylan is the major component of plant cell-wall hemicelluloses. beta-D-Xylosidases are involved in the breakdown of xylans into xylose and belong to families 3, 39, 43, 52, and 54 of glycoside hydrolases. Here, we report the first crystal structure of a member of family 39 glycoside hydrolase, i.e. beta-D-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. This study also represents the first structure of any beta-xylosidase of the above five glycoside hydrolase families. Each monomer of T. saccharolyticum beta-xylosidase comprises three distinct domains; a catalytic domain of the canonical (beta/alpha)(8)-barrel fold, a beta-sandwich domain, and a small alpha-helical domain. We have determined the structure in two forms: D-xylose-bound enzyme and a covalent 2-deoxy-2-fluoro-alpha-D-xylosyl-enzyme intermediate complex, thus providing two snapshots in the reaction pathway. This study provides structural evidence for the proposed double displacement mechanism that involves a covalent intermediate. Furthermore, it reveals possible functional roles for His228 as the auxiliary acid/base and Glu323 as a key residue in substrate recognition.

Selected figure(s)

Figure 1.
Figure 1. Overall fold of T. saccharolyticum b-xylosidase. (a) View along the (b/a)[8]-barrel axis. (b) View perpendicular to the (b/a)[8]-barrel axis. The Figures are produced with the Image -xylose-bound structure. The (b/a)[8]-barrel and the b-hairpin protruding from the catalytic domain are colored in green and yellow, respectively. The b-sandwich and the small a-helical domains are in blue and red, respectively. Ten a-helices are indicated as A to J, 19 b-strands as 1 to 19, and seven 3[10]-helices as y1 to y7. Image -Xylose is shown in a stick model. Carbon atoms are colored in black and oxygen atoms in red.

Figure 5.
Figure 5. Active site in the (2F-xylosyl)-xylosidase structure. a, Stereo view of the active site. The residues interacting with the 2F-xylosyl moiety are represented as stick models. Carbon, nitrogen, oxygen, and fluorine atoms are colored in green, blue, red, and gray, respectively. A water molecule is represented as a red ball. The (F[o] -F[c]) electron density map is contoured at 2.5s for the side-chain of Glu277, the covalently linked 2F-xylosyl moiety, and the water molecule, all of which were omitted in the map calculation. b, Schematic diagram showing the hydrogen-bonding network in the active site. The distances (in Å) averaged over the four monomers in the crystallographic asymmetric unit are indicated.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 335, 155-165) copyright 2004.

Figures were selected by an automated process.