PDBsum entry 1vbu

Hydrolase

PDB id: 1vbu

Contents

Protein chains

324 a.a. *

Ligands

SO4

ACY ×6

GOL ×2

Waters ×618

* Residue conservation analysis

PDB id:

1vbu

Name:

Hydrolase

Title:

Crystal structure of native xylanase 10b from thermotoga maritima

Structure:

Endo-1,4-beta-xylanase b. Chain: a, b. Synonym: xylanase, xylanase 10b. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.186 R-free: 0.218

Authors:

Ihsanawati,T.Kumasaka,T.Kaneko,S.Nakamura,N.Tanaka

Key ref:

Ihsanawati et al. (2005). Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8. Proteins, 61, 999. PubMed id: 16247799 DOI: 10.1002/prot.20700

Date:

02-Mar-04 Release date: 28-Jun-05

Protein chains

Q9WXS5  (Q9WXS5_THEMA) -  Beta-xylanase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 347 a.a.

Struc: 324 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.

DOI no: 10.1002/prot.20700

Proteins 61:999 (2005)

PubMed id: 16247799

Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.

Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, R.Yatsunami, T.Sato, S.Nakamura, N.Tanaka.

ABSTRACT

The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.

Selected figure(s)

Figure 1.
Figure 1. A: Overall structure of TmxB (in stereo) from the top view. Major -helices and -strands are drawn in red and green, respectively, and labeled according to the ideal ( / )[8] barrel structure.[42] The two catalytic residues are labeled and depicted by ball-and-stick facing two xylose moieties. B: Stereo view of superimposition of TmxB-xylotriose (yellow) with Psx-xylotriose (blue) in the catalytic site. Red dash lines indicate hydrogen bonds in the TmxB complex structure, which are also found in Psx. Blue dash lines represent hydrogen bonds, which are only found in Psx.

Figure 4.
Figure 4. Molecular interactions for thermal stability of TmxB. A: Aromatic interactions from the top view showing five distinct clusters drawn in different colors. B: Electrostatic interactions in the C-terminal region consist of a triad salt bridge (Asp780-Asp784-Lys836) and single ones (Lys769-Glu773, Asp798-Lys823 and Lys835-Glu839. C-E: Comparison of aromatic interactions, connecting 1, 2, 1, and 8 in TmxB, Ctx, and Pfx, respectively.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 61, 999-0) copyright 2005.

Figures were selected by an automated process.