PDBsum entry: 1h14

Hydrolase

PDB-id: 1h14

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

404 a.a. *

Waters ×356

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1h14

Name:

Hydrolase

Title:

Structure of a cold-adapted family 8 xylanase

Structure:

Endo-1,4-beta-xylanase. Chain: a. Engineered: yes. Mutation: yes

Source:

Pseudoalteromonas haloplanktis. Organism_taxid: 228. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

Q8RJN8 (Q8RJN8_PSEHA)

Seq:

Struc:

Seq:

426 a.a.

Struc:

404 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Enzyme class:

E.C.3.2.1.8   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

Resolution:

1.5Å

R-factor:

0.145

R-free:

0.171

Authors:

F.Van Petegem,T.Collins,M.A.Meuwis,G.Feller,C.Gerday, J.Van Beeumen

Key ref:

F.Van Petegem et al. (2003). The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.. J Biol Chem, 278, 7531-7539. [PubMed id: 12475991] [DOI: 10.1074/jbc.M206862200]

Date:

02-Jul-02

Release date:

13-Mar-03

Related entries:

1h12 structure of a cold-adapted family 8 xylanase
1h13 structure of a cold-adapted family 8 xylanase

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M206862200

J Biol Chem 278:7531-7539 (2003)

PubMed id: 12475991

The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.

F.Van Petegem, T.Collins, M.A.Meuwis, C.Gerday, G.Feller, J.Van Beeumen.

ABSTRACT

Enzymes from psychrophilic organisms differ from their mesophilic counterparts in having a lower thermostability and a higher specific activity at low and moderate temperatures. The current consensus is that they have an increased flexibility, enhancing accommodation and transformation of the substrates at low energy costs. Here we describe the structure of the xylanase from the Antarctic bacterium Pseudoalteromonas haloplanktis at 1.3 A resolution. Xylanases are usually grouped into glycosyl hydrolase families 10 and 11, but this enzyme belongs to family 8. The fold differs from that of other known xylanases and can be described as an (alpha/alpha)(6) barrel. Various parameters that may explain the cold-adapted properties were examined and indicated that the protein has a reduced number of salt bridges and an increased exposure of hydrophobic residues. The crystal structures of a complex with xylobiose and of mutant D144N were obtained at 1.2 and 1.5 A resolution, respectively. Analysis of the various substrate binding sites shows that the +3 and -3 subsites are rearranged as compared to those of a family 8 homolog, while the xylobiose complex suggests the existence of a +4 subsite. A decreased acidity of the substrate binding cleft and an increased flexibility of aromatic residues lining the subsites may enhance the rate at which substrate is bound.

Selected figure(s)

Figure 4.
Fig. 4. Binding of xylobiose to pXyl. A, omit map of a complex of the enzyme with xylobiose, showing the positioning of the reducing end xylose in the xylanase structure. The map is contoured at 2 (pink), 3 (blue), and 4 (green). The refined coordinates for the xylosyl residue and for Tyr-378 are shown. B, LIGPLOT diagram showing the interactions between the xylosyl residue and protein residues/water molecules (dark gray spheres). Hydrogen bonds are represented by dashed lines. The side chain of Tyr-378 is in hydrophobic contact with the C-5 atom of the xylosyl residue.

Figure 6.
Fig. 6. Schematic representation of the geometry of the catalytic center of the wild type cold-adapted xylanase (A), the psychrophilic xylanase mutant D144N (B), and the native C. thermocellum endoglucanase CelA (C). Dashed lines indicate hydrogen bonds. Distances between residues not implicated in hydrogen bonding are shown by a double arrow. Hypothetical charges are shown as + or . All distances shown are in Å. For clarity, water atoms implicated in hydrogen bonds are not included.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 7531-7539) copyright 2003.

Figures were selected by an automated process.