PDBsum entry: 1r87

Hydrolase

PDB id: 1r87

Contents

Protein chain

371 a.a. *

Ligands

XYP-XYP

XYP-XYP-XYP

SO4

Metals

_ZN ×7

_CL ×2

Waters ×303

* Residue conservation analysis

PDB id:

1r87

Name:

Hydrolase

Title:

Crystal structure of the extracellular xylanase from geobaci stearothermophilus t-6 (xt6, monoclinic form): the complex enzyme with xylopentaose at 1.67a resolution

Structure:

Endo-1,4-beta-xylanase. Chain: a. Synonym: xylanase, 1,4-beta-d-xylan xylanohydrolase, xylana engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: xyna. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.67Å R-factor: 0.169 R-free: 0.186

Authors:

M.Bar,G.Golan,G.Zolotnitsky,Y.Shoham,G.Shoham

Key ref:

G.Zolotnitsky et al. (2004). Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry. Proc Natl Acad Sci U S A, 101, 11275-11280. PubMed id: 15277671 DOI: 10.1073/pnas.0404311101

Date:

23-Oct-03 Release date: 20-Jul-04

Protein chain

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

Seq: 407 a.a.

Struc: 371 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: 10.1073/pnas.0404311101

Proc Natl Acad Sci U S A 101:11275-11280 (2004)

PubMed id: 15277671

Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry.

G.Zolotnitsky, U.Cogan, N.Adir, V.Solomon, G.Shoham, Y.Shoham.

ABSTRACT

Relating thermodynamic parameters to structural and biochemical data allows a better understanding of substrate binding and its contribution to catalysis. The analysis of the binding of carbohydrates to proteins or enzymes is a special challenge because of the multiple interactions and forces involved. Isothermal titration calorimetry (ITC) provides a direct measure of binding enthalpy (DeltaHa) and allows the determination of the binding constant (free energy), entropy, and stoichiometry. In this study, we used ITC to elucidate the binding thermodynamics of xylosaccharides for two xylanases of family 10 isolated from Geobacillus stearothermophilus T-6. The change in the heat capacity of binding (DeltaCp = DeltaH/DeltaT) for xylosaccharides differing in one sugar unit was determined by using ITC measurements at different temperatures. Because hydrophobic stacking interactions are associated with negative DeltaCp, the data allow us to predict the substrate binding preference in the binding subsites based on the crystal structure of the enzyme. The proposed positional binding preference was consistent with mutants lacking aromatic binding residues at different subsites and was also supported by tryptophan fluorescence analysis.

Selected figure(s)

Figure 3.
Fig. 3. Substrate positional binding in XT6. (A) Schematic representation of the hydrogen bonding network and stacking interactions in the XT6 binding site. (B) Structure of XT6 in complex with X[3] and X[2] (cleaved X[5]), showing only the aromatic amino acids and the sugars. Tyr-203 and Trp-273 form stacking interactions with the sugar rings at subsites +1 and +2, respectively. (C) The suggested positional binding of xylosaccharides to the binding subsites of XT6, obtained by combining the C[p] with the structural data.

Figure 5.
Fig. 5. Enthalpy-entropy compensation plot for the binding of X[2], X[3], X[4], X[5], X[6], beech wood xylan (Be), birch wood xylan (Bi), and oat spelts xylan (Oat) to IXT6 ( ) and to XT6 ( ) at 303 K. The dashed lines are the theoretical range of G[a], where the binding constants vary by three orders of magnitude.

Figures were selected by an automated process.