PDBsum entry: 1ur1

Hydrolase

PDB id: 1ur1

Contents

Protein chain

346 a.a. *

Ligands

XYS-XYP-AHR

Metals

_MG

_CL

Waters ×568

* Residue conservation analysis

PDB id:

1ur1

Name:

Hydrolase

Title:

Xylanase xyn10b mutant (e262s) from cellvibrio mixtus in complex with arabinofuranose alpha-1,3 linked to xylobiose

Structure:

Endoxylanase. Chain: a. Fragment: catalytic domain, residues 11-379. Engineered: yes. Mutation: yes. Other_details: engineered mutation glu 262 ser in coords

Source:

Cellvibrio mixtus. Organism_taxid: 39650. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.43Å R-factor: 0.153 R-free: 0.186

Authors:

G.Pell,E.J.Taylor,T.M.Gloster,J.P.Turkenburg,C.M.G.A.Fontes, L.M.A.Ferreira,G.J.Davies,H.J.Gilbert

Key ref:

G.Pell et al. (2004). The mechanisms by which family 10 glycoside hydrolases bind decorated substrates. J Biol Chem, 279, 9597-9605. PubMed id: 14668328 DOI: 10.1074/jbc.M312278200

Date:

24-Oct-03 Release date: 18-Dec-03

Protein chain

O68541  (O68541_9GAMM) -  Endoxylanase

Seq: 379 a.a.

Struc: 346 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (5 terms)

DOI no: 10.1074/jbc.M312278200

J Biol Chem 279:9597-9605 (2004)

PubMed id: 14668328

The mechanisms by which family 10 glycoside hydrolases bind decorated substrates.

G.Pell, E.J.Taylor, T.M.Gloster, J.P.Turkenburg, C.M.Fontes, L.M.Ferreira, T.Nagy, S.J.Clark, G.J.Davies, H.J.Gilbert.

ABSTRACT

Endo-beta-1,4-xylanases (xylanases), which cleave beta-1,4 glycosidic bonds in the xylan backbone, are important components of the repertoire of enzymes that catalyze plant cell wall degradation. The mechanism by which these enzymes are able to hydrolyze a range of decorated xylans remains unclear. Here we reveal the three-dimensional structure, determined by x-ray crystallography, and the catalytic properties of the Cellvibrio mixtus enzyme Xyn10B (CmXyn10B), the most active GH10 xylanase described to date. The crystal structure of the enzyme in complex with xylopentaose reveals that at the +1 subsite the xylose moiety is sandwiched between hydrophobic residues, which is likely to mediate tighter binding than in other GH10 xylanases. The crystal structure of the xylanase in complex with a range of decorated xylooligosaccharides reveals how this enzyme is able to hydrolyze substituted xylan. Solvent exposure of the O-2 groups of xylose at the +4, +3, +1, and -3 subsites may allow accommodation of the alpha-1,2-linked 4-O-methyl-d-glucuronic acid side chain in glucuronoxylan at these locations. Furthermore, the uronic acid makes hydrogen bonds and hydrophobic interactions with the enzyme at the +1 subsite, indicating that the sugar decorations in glucuronoxylan are targeted to this proximal aglycone binding site. Accommodation of 3'-linked l-arabinofuranoside decorations is observed in the -2 subsite and could, most likely, be tolerated when bound to xylosides in -3 and +4. A notable feature of the binding mode of decorated substrates is the way in which the subsite specificities are tailored both to prevent the formation of "dead-end" reaction products and to facilitate synergy with the xylan degradation-accessory enzymes such as alpha-glucuronidase. The data described in this report and in the accompanying paper indicate that the complementarity in the binding of decorated substrates between the glycone and aglycone regions appears to be a conserved feature of GH10 xylanases.

Selected figure(s)

Figure 1.
FIG. 1. Activity of CmXyn10B against xylooligosaccharides. CmXyn10B was incubated with xylotriose (A), xylotetraose (B), xylopentaose (C), and xylohexaose (D), and the reaction products generated were determined by HPLC. The reaction products generated are as follows: xylose ( ), xylobiose ( o ), xylotriose ( ), xylotetraose ( ), xylopentaose ( ), and xylohexaose ( ).

Figure 4.
FIG. 4. Schematic representation of the C. mixtus Xyn10B complexes. The schematic provides insight into the binding mode of xylopentaose, MX[3] and AX[3] bound in the substrate binding cleft of CmXyn10B, for which electron density is shown in Figs. 2 and 5. Note that residues that are not apparent in each substrate are disordered in the crystal structure.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 9597-9605) copyright 2004.

Figures were selected by an automated process.