PDBsum entry 2z8s

Lyase

PDB id: 2z8s

Contents

Protein chains

583 a.a. *

Ligands

ADA-ADA ×2

Metals

_CA ×20

Waters ×335

* Residue conservation analysis

PDB id:

2z8s

Name:

Lyase

Title:

Crystal structure of rhamnogalacturonan lyase yesw complexed with digalacturonic acid

Structure:

Yesw protein. Chain: a, b. Fragment: unp residues 38-620. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: yesw. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.166 R-free: 0.242

Authors:

A.Ochiai,T.Itoh,Y.Maruyama,A.Kawamata,B.Mikami,W.Hashimoto,K.Murata

Key ref:

A.Ochiai et al. (2007). A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER. J Biol Chem, 282, 37134-37145. PubMed id: 17947240 DOI: 10.1074/jbc.M704663200

Date:

10-Sep-07 Release date: 16-Oct-07

Protein chains

O31526  (YESW_BACSU) -  Rhamnogalacturonan endolyase YesW from Bacillus subtilis (strain 168)

Seq: 620 a.a.

Struc: 583 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.2.23 - rhamnogalacturonan endolyase.

DOI no: 10.1074/jbc.M704663200

J Biol Chem 282:37134-37145 (2007)

PubMed id: 17947240

A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER.

A.Ochiai, T.Itoh, Y.Maruyama, A.Kawamata, B.Mikami, W.Hashimoto, K.Murata.

ABSTRACT

Rhamnogalacturonan (RG) lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls. An extracellular RG lyase YesW from saprophytic Bacillus subtilis is a member of polysaccharide lyase family 11 and cleaves glycoside bonds in polygalacturonan as well as RG type-I through a beta-elimination reaction. Crystal structures of YesW and its complex with galacturonan disaccharide, a reaction product analogue, were determined at 1.4 and 2.5A resolutions with final R-factors of 16.4% and 16.6%, respectively. The enzyme is composed of an eight-bladed beta-propeller with a deep cleft in the center as a basic scaffold, and its structural fold has not been seen in polysaccharide lyases analyzed thus far. Structural analysis of the disaccharide-bound YesW and a site-directed mutagenesis study suggested that Arg-452 and Lys-535 stabilize the carboxyl group of the acidic polysaccharide molecule and Tyr-595 makes a stack interaction with the sugar pyranose ring. In addition to amino acid residues binding to the disaccharide, one calcium ion, which is coordinated by Asp-401, Glu-422, His-363, and His-399, may mediate the enzyme activity. This is, to our knowledge, the first report of a new structural category with a beta-propeller fold in polysaccharide lyases and provides structural insights into substrate binding by RG lyase.

Selected figure(s)

Figure 2.
FIGURE 2. Structure of YesW. A, overall structure (stereodiagram). B, image A is turned by 90 degrees around the x-axis. C, topology diagram. β-Sheets are shown as blue or green arrows and helices as pink cylinders. Calcium ions are shown as red balls.

Figure 3.
FIGURE 3. Calcium-binding sites of YesW. A, calcium ions are included in each blade of the β-propeller. Detailed coordination of calcium ions in blades B and E is shown in the upper and lower insets, respectively. B, two calcium ions are included in the central space of the β-propeller. Their detailed coordination is shown in the upper and lower insets. Calcium ions are shown as red balls.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 37134-37145) copyright 2007.

Figures were selected by an automated process.