PDBsum entry 2dfc

Hydrolase

PDB id: 2dfc

Contents

Protein chain

190 a.a. *

Metals

IOD

Waters ×208

* Residue conservation analysis

PDB id:

2dfc

Name:

Hydrolase

Title:

Xylanase ii from tricoderma reesei at 293k

Structure:

Endo-1,4-beta-xylanase 2. Chain: a. Synonym: xylanase 2, 1,4-beta-d-xylan xylanohydrolase 2. Ec: 3.2.1.8

Source:

Hypocrea jecorina. Organism_taxid: 51453

Resolution:

1.19Å R-factor: 0.106 R-free: 0.122

Authors:

K.Harata,T.Akiba

Key ref:

N.Watanabe et al. (2006). Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement. Acta Crystallogr D Biol Crystallogr, 62, 784-792. PubMed id: 16790934 DOI: 10.1107/S0907444906017379

Date:

28-Feb-06 Release date: 11-Jul-06

Protein chain

P36217  (XYN2_HYPJR) -  Endo-1,4-beta-xylanase 2 from Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30)

Seq: 223 a.a.

Struc: 190 a.a.*

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

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.

DOI no: 10.1107/S0907444906017379

Acta Crystallogr D Biol Crystallogr 62:784-792 (2006)

PubMed id: 16790934

Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement.

N.Watanabe, T.Akiba, R.Kanai, K.Harata.

ABSTRACT

An orthorhombic crystal of xylanase II from Trichoderma reesei was grown in the presence of sodium iodide. Crystal structures at atomic resolution were determined at 100 and 293 K. Protein molecules were aligned along a crystallographic twofold screw axis, forming a helically extended polymer-like chain mediated by an iodide ion. The iodide ion connected main-chain peptide groups between two adjacent molecules by an N-H...I-...H-N hydrogen-bond bridge, thus contributing to regulation of the molecular arrangement and suppression of the rigid-body motion in the crystal with high diffraction quality. The structure at 293 K showed considerable thermal motion in the loop regions connecting the beta-strands that form the active-site cleft. TLS model analysis of the thermal motion and a comparison between this structure and that at 100 K suggest that the fluctuation of these loop regions is attributable to the hinge-like movement of the beta-strands.

Selected figure(s)

Figure 4.
Figure 4 A stereoscopic view of hydrogen-bonding contacts of iodide ions drawn with ORTEP-III (Burnett & Johnson, 1996[Burnett, M. N. & Johnson, C. K. (1996). ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations. Report ORNL-6895, Oak Ridge National Laboratory, Oak Ridge, TN, USA.]). Thermal ellipsoids are drawn with 30% probability. The asterisks denote amino-acid residues of an adjacent molecule.

Figure 7.
Figure 7 Distance difference map (a) showing the movement of C^ atoms between the structures at 100 and 293 K. The distance difference was calculated as the difference between the distances of C^ atoms as r = C}_{\alpha}}] (100 K) - C}_{\alpha}}] (293 K). Contours are drawn in the region from -0.4 to -1.8 Å with an interval of 0.2 Å. Loop regions corresponding to the `fingertips' are denoted by T for the `thumb' and A, B, C and D for the four `fingers'. Schematic drawing of the energy landscape (b) shows the change of the population of the atomic position of the `fingertip' regions induced by cooling from 293 to 100 K. An average position is denoted by x.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 784-792) copyright 2006.

Figures were selected by the author.