PDBsum entry: 1clx

Xylanase

PDB id: 1clx

Contents

Protein chains

345 a.a. *

Metals

_CA ×4

Waters ×1108

* Residue conservation analysis

PDB id:

1clx

Name:

Xylanase

Title:

Catalytic core of xylanase a

Structure:

Xylanase a. Chain: a, b, c, d. Fragment: catalytic core, residues 264 - 611. Engineered: yes

Source:

Cellvibrio japonicus. Organism_taxid: 155077. Strain: cellulosa. Gene: truncated xyna (codons 264-611. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.166

Authors:

G.W.Harris,J.A.Jenkins,I.Connerton,R.W.Pickersgill

Key ref:

G.W.Harris et al. (1996). Refined crystal structure of the catalytic domain of xylanase A from Pseudomonas fluorescens at 1.8 A resolution. Acta Crystallogr D Biol Crystallogr, 52, 393-401. PubMed id: 15299710 DOI: 10.1107/S0907444995013540

Date:

31-Aug-95 Release date: 20-Jun-96

Protein chains

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

Seq: 611 a.a.

Struc: 345 a.a.

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: 10.1107/S0907444995013540

Acta Crystallogr D Biol Crystallogr 52:393-401 (1996)

PubMed id: 15299710

Refined crystal structure of the catalytic domain of xylanase A from Pseudomonas fluorescens at 1.8 A resolution.

G.W.Harris, J.A.Jenkins, I.Connerton, R.W.Pickersgill.

ABSTRACT

The three-dimensional structure of native xylanase A from Pseudomonas flouorescens subspecies cellulosa has been refined at 1.8 A resolution. The space group is P2(1)2(1)2(1) with four molecules in the asymmetric unit. The final model has an R factor of 0.166 for 103 749 reflections with the four molecules refined independently. The tertiary structure consists of an eightfold beta/alpha-barrel, the so-called TIM-barrel fold. The active site is in an open cleft at the carboxy-terminal end of the beta/alpha-barrel, and the active-site residues are a pair of glutamates, Glu127 on strand 4 and Glu246 on strand 7. Both these catalytic glutamate residues are found on beta-bulges. An atypically long loop after strand 7 is stabilized by calcium. Unusual features include a non-proline cis-peptide residue Ala80 which is found on a beta-bulge at the end of beta-strand 3. The three beta-bulge type distortions occurring on beta-strands 3, 4 and 7 are functionally significant as they serve to orient important active-site residues. The active-site residues are further held in place by an extensive hydrogen-bonding network of active-site residues in the catalytic site of xylanase A. A chain of well ordered water molecules occupies the substrate-binding cleft, some or all of which are expelled on binding of the substrate.

Selected figure(s)

Figure 1.
Fig. 1. The eightfold fl/ot-barrel of xylanase A viewed perpendicular to the barrel axis showing the acid base Glu127 on strand 4 and the nucleophile lu246 on strand 7. The Ca atom (yellow dot) stabilizes the long loop after strand 7. This figure was prepared using MOLSCRIPT (Kraulis, 1991). The/J-strands are shown as arrows in red and the eight ot-helicies are shown in green; the additional or-helix (ot4a) is shown in yellow. The glutamates re 5.5 ,~ apart consistent with a retention of the onfiguration uring catalysis.

Figure 6.
Fig. 6. The/3-bulge features in xylanase A. (a) /3-strand 6: 13- bulge involving residues Thr245 and nucleophile Glu246. (b) /3- strand 4: double /3-bule crankshaft feature involving the residues Vail24, Vail25, Asn126 and acid-base catalyst Glu127. (c)/3-strand 3: /3-bulge (His79 and cis-Ala80) followed by a /3-tum involving residues Ala80 Leu1, Va182 and Trp83. The space under Gly78 is filled by the side chain of Trp122 on the adjacent/3-strand/34. The neighbouring residue Asp123 makes hydrogen bonds with both His77 and His7.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 393-401) copyright 1996.

Figures were selected by an automated process.