3IWR

Crystal structure of class I chitinase from Oryza sativa L. japonica

Summary for 3IWR

• Entry DOI: 10.2210/pdb3iwr/pdb
• Related: 2DKV
• Descriptor: Chitinase, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
• Functional Keywords: class i chitinase, oryza sativa l. japonica, chitin-binding, glycosidase, hydrolase
• Biological source: Oryza sativa Japonica Group (Japanese rice)
• Total number of polymer chains: 2
• Total formula weight: 66107.26

Authors

Kezuka, Y.,Watanabe, T.,Nonaka, T. (deposition date: 2009-09-03, release date: 2010-04-21, Last modification date: 2024-10-16)

Primary citation

Kezuka, Y.,Kojima, M.,Mizuno, R.,Suzuki, K.,Watanabe, T.,Nonaka, T.
Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering.
Proteins, 78:2295-2305, 2010

PubMed Abstract: The rice class I chitinase OsChia1b, also referred to as RCC2 or Cht-2, is composed of an N-terminal chitin-binding domain (ChBD) and a C-terminal catalytic domain (CatD), which are connected by a proline- and threonine-rich linker peptide. Because of the ability to inhibit fungal growth, the OsChia1b gene has been used to produce transgenic plants with enhanced disease resistance. As an initial step toward elucidating the mechanism of hydrolytic action and antifungal activity, the full-length structure of OsChia1b was analyzed by X-ray crystallography and small-angle X-ray scattering (SAXS). We determined the crystal structure of full-length OsChia1b at 2.00-A resolution, but there are two possibilities for a biological molecule with and without interdomain contacts. The SAXS data showed an extended structure of OsChia1b in solution compared to that in the crystal form. This extension could be caused by the conformational flexibility of the linker. A docking simulation of ChBD with tri-N-acetylchitotriose exhibited a similar binding mode to the one observed in the crystal structure of a two-domain plant lectin complexed with a chitooligosaccharide. A hypothetical model based on the binding mode suggested that ChBD is unsuitable for binding to crystalline alpha-chitin, which is a major component of fungal cell walls because of its collisions with the chitin chains on the flat surface of alpha-chitin. This model also indicates the difference in the binding specificity of plant and bacterial ChBDs of GH19 chitinases, which contribute to antifungal activity.

PubMed: 20544965
DOI: 10.1002/prot.22742

Experimental method

X-RAY DIFFRACTION (2.57 Å)