PDBsum entry: 1hiz

Glycosidase

PDB id: 1hiz

Contents

Protein chain

375 a.a. *

Ligands

GLA

GLC

SO4

Waters ×630

* Residue conservation analysis

PDB id:

1hiz

Name:

Glycosidase

Title:

Xylanase t6 (xt6) from bacillus stearothermophilus

Structure:

Endo-1,4-beta-xylanase. Chain: a. Engineered: yes

Source:

Bacillus stearothermophilus. Organism_taxid: 1422. Strain: ncimb40221. Cell: bacteria. Cellular_location: extra cellular. Gene: xyna. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_cell: bacteria.

Resolution:

2.4Å R-factor: 0.158 R-free: 0.188

Authors:

G.Sainz,A.Tepplitsky,V.Stojanoff,A.Thompson,Y.Shoham, G.Shoham

Key ref:

A.Teplitsky et al. (2004). Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing. Acta Crystallogr D Biol Crystallogr, 60, 836-848. PubMed id: 15103129 DOI: 10.1107/S0907444904004123

Date:

05-Jan-01 Release date: 04-Jan-02

Protein chain

P40943  (XYN1_GEOSE) -  Endo-1,4-beta-xylanase

Seq: 407 a.a.

Struc: 375 a.a.

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 

• Cellular component: extracellular region (1 term)
• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (6 terms)

DOI no: 10.1107/S0907444904004123

Acta Crystallogr D Biol Crystallogr 60:836-848 (2004)

PubMed id: 15103129

Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing.

A.Teplitsky, A.Mechaly, V.Stojanoff, G.Sainz, G.Golan, H.Feinberg, R.Gilboa, V.Reiland, G.Zolotnitsky, D.Shallom, A.Thompson, Y.Shoham, G.Shoham.

ABSTRACT

Xylanases are hemicellulases that hydrolyze the internal beta-1,4-glycoside bonds of xylan. The extracellular thermostable endo-1,4-beta-xylanase (EC 3.2.1.8; XT6) produced by the thermophilic bacterium Geobacillus stearothermophilus T-6 was shown to bleach pulp optimally at pH 9 and 338 K and was successfully used in a large-scale biobleaching mill trial. The xylanase gene was cloned and sequenced. The mature enzyme consists of 379 amino acids, with a calculated molecular weight of 43 808 Da and a pI of 9.0. Crystallographic studies of XT6 were performed in order to study the mechanism of catalysis and to provide a structural basis for the rational introduction of enhanced thermostability by site-specific mutagenesis. XT6 was crystallized in the primitive trigonal space group P3(2)21, with unit-cell parameters a = b = 112.9, c = 122.7 A. A full diffraction data set for wild-type XT6 has been measured to 2.4 A resolution on flash-frozen crystals using synchrotron radiation. A fully exchanged selenomethionyl XT6 derivative (containing eight Se atoms per XT6 molecule) was also prepared and crystallized in an isomorphous crystal form, providing full selenium MAD data at three wavelengths and enabling phase solution and structure determination. The structure of wild-type XT6 was refined at 2.4 A resolution to a final R factor of 15.6% and an R(free) of 18.6%. The structure demonstrates that XT6 is made up of an eightfold TIM-barrel containing a deep active-site groove, consistent with its 'endo' mode of action. The two essential catalytic carboxylic residues (Glu159 and Glu265) are located at the active site within 5.5 A of each other, as expected for 'retaining' glycoside hydrolases. A unique subdomain was identified in the carboxy-terminal part of the enzyme and was suggested to have a role in xylan binding. The three-dimensional structure of XT6 is of great interest since it provides a favourable starting point for the rational improvement of its already high thermal and pH stabilities, which are required for a number of biotechnological and industrial applications.

Selected figure(s)

Figure 7.
Figure 7 Structural comparison of XT6 (green) with the xylanase from Pe. simplicissimum (XlnA, magenta). The superposition is based on the key atoms described in the text. (a) Top view showing the similarity of the two structures in the central ( / )[8]-barrel. (b) Side view showing the differences between the two structures, mainly around the unique subdomain of XT6 (top left). (c) A zoom into the active site of the two enzymes, demonstrating the almost identical arrangement of the two catalytic glutamic residues (Glu159 and Glu265 in XT6 and Glu132 and Glu238 in XlnA).

Figure 8.
Figure 8 The solvent-accessible surface of the xylanases from G. stearothermophilus (XT6, left) and Pe. simplicissimum (XlnA, right) coloured according to electrostatic potential (positive in blue, negative in red and neutral in grey). (a) Top view, demonstrating the differences in shape and charge distribution around the substrate-binding cavity. (b) Side view, showing the unique subdomain and the increased depth of the TIM-barrel in XT6.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 836-848) copyright 2004.

Figures were selected by an automated process.