PDBsum entry: 1f5j

Hydrolase

PDB id: 1f5j

Contents

Protein chains

199 a.a. *

Ligands

SO4 ×2

Waters ×294

* Residue conservation analysis

PDB id:

1f5j

Name:

Hydrolase

Title:

Crystal structure of xynb, a highly thermostable beta-1,4- xylanase from dictyoglomus thermophilum rt46b.1, at 1.8 a resolution

Structure:

Beta-1,4-xylanase. Chain: a, b. Engineered: yes

Source:

Dictyoglomus thermophilum. Organism_taxid: 14. Strain: rt46b.1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.185 R-free: 0.222

Authors:

A.A.Mccarthy,E.N.Baker

Key ref:

A.A.McCarthy et al. (2000). Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution. Acta Crystallogr D Biol Crystallogr, 56, 1367-1375. PubMed id: 11053833 DOI: 10.1107/S0907444900009896

Date:

26-Jul-00 Release date: 15-Nov-00

Protein chains

P77853  (P77853_DICTH) -  Endo-1,4-beta-xylanase

Seq: 360 a.a.

Struc: 199 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.8 - Endo-1,4-beta-xylanase.
• Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: hydrolase activity, hydrolyzing O-glycosyl compounds (1 term)

DOI no: 10.1107/S0907444900009896

Acta Crystallogr D Biol Crystallogr 56:1367-1375 (2000)

PubMed id: 11053833

Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution.

A.A.McCarthy, D.D.Morris, P.L.Bergquist, E.N.Baker.

ABSTRACT

Microorganisms employ a large array of enzymes to break down the cellulose and hemicelluloses of plant biomass. These enzymes, especially those with high thermal stability, have many uses in biotechnology. We have solved the crystal structure of a beta-1, 4-xylanase, XynB, from the extremely thermophilic bacterium Dictyoglomus thermophilum, isolate Rt46B.1. The protein crystallized from 1.6 M ammonium sulfate, 0.2 M HEPES pH 7.2 and 10% glycerol, with unit-cell parameters a = b = 91.3, c = 44.9 A and space group P4(3). The structure was solved at high resolution (1.8 A) by X-ray crystallography, using the method of isomorphous replacement with a single mercury derivative, and refined to a final R factor of 18.3% (R(free) = 22.1%). XynB has the single-domain fold typical of family 11 xylanases, comprising a jelly roll of two highly twisted beta-sheets that create a deep substrate-binding cleft. The two catalytic residues, Glu90 and Glu180, occupy this cleft. Compared with other family 11 xylanases, XynB has a greater proportion of polar surface and has a slightly extended C-terminus that, combined with the extension of beta-strand A5, gives additional hydrogen bonding and hydrophobic packing. These factors may account for the enhanced thermal stability of the enzyme.

Selected figure(s)

Figure 3.
Figure 3 Stereo figure showing the electron density in the vicinity of the two cysteine residues Cys79 and Cys178; the side chain of Cys178 is oriented away from Cys79 such that no disulfide bond is formed. Electron density taken from the final 2F[o] - F[c] map contoured at a level of 1.5 .

Figure 4.
Figure 4 Stereo diagram showing the structure in the vicinity of the insertion in the B3-A5 loop in XynB from D. thermophilum. In XynB (blue) this loop, including the 3[10]-helix 55-59, folds in against the body of the molecule such that an extended hydrophobic core, including Tyr52, Leu59 and Ile62, is covered by the partly buried Trp56 from the centre of the loop. Phe195 from the extended C-terminus (top of picture) can also be seen, inserting into the core and tying down the C-terminal strand (C). In contrast, in the P. varioti xylanase (gold) and B. circulans xylanase (green) xylanases, the loop is five residues shorter and includes several exposed hydrophobic residues (not shown). The disulfide bond 110-154, which links the helix to strand B9 in the P. varioti xylanase and has been associated with enhanced thermostability, is also shown (yellow spheres).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 1367-1375) copyright 2000.

Figures were selected by the author.