PDBsum entry 2d24

Hydrolase

PDB id: 2d24

Contents

Protein chains

427 a.a. *

Ligands

XYS-XYS-XYS-XYS-XYS ×2

XYS-XYS-XYS-XYS

XYS-XYS ×2

SO4 ×2

GOL ×3

Waters ×672

* Residue conservation analysis

PDB id:

2d24

Name:

Hydrolase

Title:

Crystal structure of es complex of catalytic-site mutant xylanase from streptomyces olivaceoviridis e-86

Structure:

Endo-1,4-beta-d-xylanase. Chain: a, b. Synonym: glycoside hydrolase family 10 xylanase. Engineered: yes. Mutation: yes

Source:

Streptomyces olivaceoviridis. Organism_taxid: 1921. Strain: e-86. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.85Å R-factor: 0.177 R-free: 0.199

Authors:

R.Suzuki,A.Kuno,Z.Fujimoto,S.Ito,S.I.Kawahara,S.Kaneko,T.Hasegawa, K.Taira

Key ref:

R.Suzuki et al. (2009). Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86. J Biochem (tokyo), 146, 61-70. PubMed id: 19279191

Date:

02-Sep-05 Release date: 10-Oct-06

Protein chains

Q7SI98  (Q7SI98_STROI) -  Beta-xylanase from Streptomyces olivaceoviridis

Seq: 436 a.a.

Struc: 427 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.

J Biochem (tokyo) 146:61-70 (2009)

PubMed id: 19279191

Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.

R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, A.Kuno.

ABSTRACT

Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can be visualized by inactivating deglycosylation step and/or using substrate analogues to isolate covalent intermediates. Furthermore, during structural analyses of glycosyl hydrolases with hydrolytic reaction products by the conventional soaking method, mutarotation of an anomeric carbon in the reaction products promptly and certainly occurs. This undesirable structural alteration hinders visualization of the second step in the reaction. Here, we investigated X-ray crystallographic visualization as a possible method for visualizing the conformational itinerary of a retaining xylanase from Streptomyces olivaceoviridis E-86. To clearly define the stereochemistry at the anomeric carbon during the deglycosylation step, extraneous nucleophiles, such as azide, were adopted to substitute for the missing base catalyst in an appropriate mutant. The X-ray crystallographic visualization provided snapshots of the components of the entire reaction, including the E*S complex, the covalent intermediate, breakdown of the intermediate and the enzyme-product (E*P)complex.