PDBsum entry 2c1f

Hydrolase

PDB id: 2c1f

Contents

Protein chain

219 a.a. *

Metals

_CD ×2

Waters ×173

* Residue conservation analysis

PDB id:

2c1f

Name:

Hydrolase

Title:

The structure of the family 11 xylanase from neocallimastix patriciarum

Structure:

Bifunctional endo-1,4-beta-xylanase a. Chain: a. Fragment: domain 2, residues 275-499. Synonym: endo-1,4-beta-xylanase a, xyla. Engineered: yes

Source:

Neocallimastix patriciarum. Organism_taxid: 4758. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.168 R-free: 0.205

Authors:

J.W.Murray,R.J.Lewis,H.J.Gilbert

Key ref:

M.Vardakou et al. (2008). Understanding the structural basis for substrate and inhibitor recognition in eukaryotic GH11 xylanases. J Mol Biol, 375, 1293-1305. PubMed id: 18078955 DOI: 10.1016/j.jmb.2007.11.007

Date:

14-Sep-05 Release date: 13-Feb-07

Protein chain

P29127  (XYNA_NEOPA) -  Bifunctional endo-1,4-beta-xylanase A from Neocallimastix patriciarum

Seq: 607 a.a.

Struc: 219 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.

DOI no: 10.1016/j.jmb.2007.11.007

J Mol Biol 375:1293-1305 (2008)

PubMed id: 18078955

Understanding the structural basis for substrate and inhibitor recognition in eukaryotic GH11 xylanases.

M.Vardakou, C.Dumon, J.W.Murray, P.Christakopoulos, D.P.Weiner, N.Juge, R.J.Lewis, H.J.Gilbert, J.E.Flint.

ABSTRACT

Endo-beta1,4-xylanases (xylanases) hydrolyse the beta1,4 glycosidic bonds in the backbone of xylan. Although xylanases from glycoside hydrolase family 11 (GH11) have been extensively studied, several issues remain unresolved. Thus, the mechanism by which these enzymes hydrolyse decorated xylans is unclear and the structural basis for the variation in catalytic activity within this family is unknown. Furthermore, the mechanism for the differences in the inhibition of fungal GH11 enzymes by the wheat protein XIP-I remains opaque. To address these issues we report the crystal structure and biochemical properties of the Neocallimastix patriciarum xylanase NpXyn11A, which displays unusually high catalytic activity and is one of the few fungal GH11 proteins not inhibited by XIP-I. Although the structure of NpXyn11A could not be determined in complex with substrates, we have been able to investigate how GH11 enzymes hydrolyse decorated substrates by solving the crystal structure of a second GH11 xylanase, EnXyn11A (encoded by an environmental DNA sample), bound to ferulic acid-1,5-arabinofuranose-alpha1,3-xylotriose (FAX(3)). The crystal structure of the EnXyn11A-FAX(3) complex shows that solvent exposure of the backbone xylose O2 and O3 groups at subsites -3 and +2 allow accommodation of alpha1,2-linked 4-methyl-D-glucuronic acid and L-arabinofuranose side chains. Furthermore, the ferulated arabinofuranose side chain makes hydrogen bonds and hydrophobic interactions at the +2 subsite, indicating that the decoration may represent a specificity determinant at this aglycone subsite. The structure of NpXyn11A reveals potential -3 and +3 subsites that are kinetically significant. The extended substrate-binding cleft of NpXyn11A, compared to other GH11 xylanases, may explain why the Neocallimastix enzyme displays unusually high catalytic activity. Finally, the crystal structure of NpXyn11A shows that the resistance of the enzyme to XIP-I is not due solely to insertions in the loop connecting beta strands 11 and 12, as suggested previously, but is highly complex.

Selected figure(s)

Figure 4.
Figure 4. The interactions between EnXyn11A and FAX[3.] The subsites are labelled, the broken lines represent hydrogen bonding interactions, and the interatomic distances are noted. (a) The glycone and (b) the aglycone region of the active site.

Figure 6.
Figure 6. Overlay of the XIP-I/P. funiculosum GH11 xylanase complex with wild-type and mutant NpXyn11A. (a) The structure of the XIP-I (green)/P. funiculosum GH11 xylanase (red) complex was overlaid with wild-type NpXyn11A (cyan). The loops connecting β strand 3 with 4 and β strand 11 with 12 appear to clash with the xylanase inhibitor. (b) Wild-type NpXyn11 (cyan) and the Δ3-4NpXyn11A mutant (magenta) were overlaid with the structure of XIP-I when in complex with the P. funiculosum GH11 xylanase. The mutation has reduced the size of the loop connecting β strands 3 and 4, which now no longer make steric clashes with XIP-I.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 375, 1293-1305) copyright 2008.

Figures were selected by an automated process.