1XYF

ENDO-1,4-BETA-XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS

PDB DOI: 10.2210/pdb1XYF/pdb

Classification: HYDROLASE
Organism(s): Streptomyces olivaceoviridis
Mutation(s): No

Deposited: 1999-05-11 Released: 2000-05-10
Deposition Author(s): Fujimoto, Z., Mizuno, H., Kuno, A., Kusakabe, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.235
R-Value Work: 0.197

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain.

Fujimoto, Z., Kuno, A., Kaneko, S., Yoshida, S., Kobayashi, H., Kusakabe, I., Mizuno, H.

(2000) J Mol Biol 300: 575-585

PubMed: 10884353 Search on PubMed
DOI: 10.1006/jmbi.2000.3877
Primary Citation of Related Structures:
1XYF

PubMed Abstract:

Xylanases hydrolyse the beta-1,4-glycosidic bonds within the xylan backbone and belong to either family 10 or 11 of the glycoside hydrolases, on the basis of the amino acid sequence similarities of their catalytic domains. Generally, xylanases have a core catalytic domain, an N and/or C-terminal substrate-binding domain and a linker region. Until now, X-ray structural analyses of family 10 xylanases have been reported only for their catalytic domains and do not contain substrate-binding domains. We have determined the crystal structure of a family 10 xylanase containing the xylan-binding domain (XBD) from Streptomyces olivaceoviridis E-86 at 1.9 A resolution. The catalytic domain comprises a (beta/alpha)(8)-barrel topologically identical to other family 10 xylanases. XBD has three similar subdomains, as suggested from a triple-repeat sequence, which are assembled against one another around a pseudo-3-fold axis, forming a galactose-binding lectin fold similar to ricin B-chain. The Gly/Pro-rich linker region connecting the catalytic domain and XBD is not visible in the electron density map, probably because of its flexibility. The interface of the two domains in the crystal is hydrophilic, where five direct hydrogen bonds and water-mediated hydrogen bonds exist. The sugar-binding residues seen in ricin/lactose complex are spatially conserved among the three subdomains in XBD, suggesting that all of the subdomains in XBD have the capacity to bind sugars. The flexible linker region enables the two domains to move independently and may provide a triple chance of substrate capturing and catalysis. The structure reported here represents an example where the metabolic enzyme uses a ricin-type lectin motif for capturing the insoluble substrate and promoting catalysis.

Related Citations:

Crystallization and Preliminary X-Ray Crystallographic Study of Streptomyces olivaceoviridis E-86 Xylanase
Fujimoto, Z., Mizuno, H., Kuno, A., Yoshida, S., Kobayashi, H., Kusakabe, I.
(1997) J Biochem 121: 826

Organizational Affiliation:

Department of Biotechnology, National Institute of Agrobiological Resources, Tsukuba, IIbaraki, 305-8602, Japan. zui@abr.affrc.go.jp

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE	A, B	436	Streptomyces olivaceoviridis	Mutation(s): 0 EC: 3.2.1.8
UniProt
Find proteins for Q7SI98 (Streptomyces olivaceoviridis) Explore Q7SI98 Go to UniProtKB: Q7SI98
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SI98
Protein Feature View Expand
Reference Sequence