2Z8R

Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution

Summary for 2Z8R

• Entry DOI: 10.2210/pdb2z8r/pdb
• Related: 2Z8S
• Descriptor: YesW protein, CALCIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
• Functional Keywords: beta-propeller, lyase
• Biological source: Bacillus subtilis
• Cellular location: Secreted: O31526
• Total number of polymer chains: 2
• Total formula weight: 131023.57

Authors

Ochiai, A.,Itoh, T.,Maruyama, Y.,Kawamata, A.,Mikami, B.,Hashimoto, W.,Murata, K. (deposition date: 2007-09-10, release date: 2007-10-16, Last modification date: 2024-03-13)

Primary citation

Ochiai, A.,Itoh, T.,Maruyama, Y.,Kawamata, A.,Mikami, B.,Hashimoto, W.,Murata, K.
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, 2007

PubMed 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 2.5 A 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.

PubMed: 17947240
DOI: 10.1074/jbc.M704663200

Experimental method

X-RAY DIFFRACTION (1.4 Å)