PDBsum entry: 1e5n

Glycosyl hydrolase

PDB id: 1e5n

Contents

Protein chains

346 a.a. *

Ligands

XYP-XYP-XYP-XYP-XYP ×2

Metals

_CA ×2

* Residue conservation analysis

PDB id:

1e5n

Name:

Glycosyl hydrolase

Title:

E246c mutant of p fluorescens subsp. Cellulosa xylanase a in complex with xylopentaose

Structure:

Endo-1,4-beta-xylanase a. Chain: a, b. Fragment: catalytic domain residues 264-611. Synonym: xylanase a. Engineered: yes. Mutation: yes. Other_details: truncated catalytic domain, aa 264-611

Source:

Pseudomonas fluorescens. Organism_taxid: 294. Variant: subsp cellulosa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Monomer (from PDB file)

Resolution:

3.2Å R-factor: 0.190 R-free: 0.245

Authors:

L.Lo Leggio,J.A.Jenkins,G.W.Harris,R.W.Pickersgill

Key ref:

L.L.Leggio et al. (2000). X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A. Proteins, 41, 362-373. PubMed id: 11025547 DOI: 10.1002/1097-0134(20001115)41:3<362::AID-PROT80>3.0.CO;2-N

Date:

27-Jul-00 Release date: 08-Dec-00

Protein chains

P14768  (XYNA_CELJU) -  Endo-1,4-beta-xylanase A

Seq: 611 a.a.

Struc: 346 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.

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: catalytic activity (3 terms)

DOI no: 10.1002/1097-0134(20001115)41:3<362::AID-PROT80>3.0.CO;2-N

Proteins 41:362-373 (2000)

PubMed id: 11025547

X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.

L.L.Leggio, J.Jenkins, G.W.Harris, R.W.Pickersgill.

ABSTRACT

The structure of the complex between a catalytically compromised family 10 xylanase and a xylopentaose substrate has been determined by X-ray crystallography and refined to 3.2 A resolution. The substrate binds at the C-terminal end of the eightfold betaalpha-barrel of Pseudomonas fluorescens subsp. cellulosa xylanase A and occupies substrate binding subsites -1 to +4. Crystal contacts are shown to prevent the expected mode of binding from subsite -2 to +3, because of steric hindrance to subsite -2. The loss of accessible surface at individual subsites on binding of xylopentaose parallels well previously reported experimental measurements of individual subsites binding energies, decreasing going from subsite +2 to +4. Nine conserved residues contribute to subsite -1, including three tryptophan residues forming an aromatic cage around the xylosyl residue at this subsite. One of these, Trp 313, is the single residue contributing most lost accessible surface to subsite -1, and goes from a highly mobile to a well-defined conformation on binding of the substrate. A comparison of xylanase A with C. fimi CEX around the +1 subsite suggests that a flatter and less polar surface is responsible for the better catalytic properties of CEX on aryl substrates. The view of catalysis that emerges from combining this with previously published work is the following: (1) xylan is recognized and bound by the xylanase as a left-handed threefold helix; (2) the xylosyl residue at subsite -1 is distorted and pulled down toward the catalytic residues, and the glycosidic bond is strained and broken to form the enzyme-substrate covalent intermediate; (3) the intermediate is attacked by an activated water molecule, following the classic retaining glycosyl hydrolase mechanism.

Selected figure(s)

Figure 3.
Figure 3. LIGPLOT diagram of XYLA E246C-XP interactions. The cut-offs for hydrogen bonding and hydrophobic contacts were 3.6 Å and 4.0 Å, respectively.

Figure 4.
Figure 4. Buried accessible surface in the complex on binding of XP to XYLA E246C.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2000, 41, 362-373) copyright 2000.

Figures were selected by an automated process.