4ASM

Crystal structure of the catalytic domain of beta-agarase D from Zobellia galactanivorans

4ASM の概要

• エントリーDOI: 10.2210/pdb4asm/pdb
• 分子名称: BETA-AGARASE D, CALCIUM ION, IMIDAZOLE, ... (5 entities in total)
• 機能のキーワード: hydrolase, glycoside hydrolase, endo-beta-agarase
• 由来する生物種: ZOBELLIA GALACTANIVORANS
• 細胞内の位置: Secreted : D7GXG4
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 41323.83

構造登録者

Hehemann, J.H.,Correc, G.,Bernard, T.,Michel, G.,Czjzek, M. (登録日: 2012-05-02, 公開日: 2012-07-25, 最終更新日: 2023-12-20)

主引用文献

Hehemann, J.H.,Correc, G.,Thomas, F.,Bernard, T.,Barbeyron, T.,Jam, M.,Helbert, W.,Michel, G.,Czjzek, M.
Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System from the Marine Bacterium Zobellia Galactanivorans.
J.Biol.Chem., 287:30571-, 2012

PubMed Abstract: Zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably, this marine Bacteroidetes possesses a complex agarolytic system comprising four β-agarases and five β-porphyranases, all belonging to the glycoside hydrolase family 16. Although β-agarases are specific for the neutral agarobiose moieties, the recently discovered β-porphyranases degrade the sulfated polymers found in various quantities in natural agars. Here, we report the biochemical and structural comparison of five β-porphyranases and β-agarases from Z. galactanivorans. The respective degradation patterns of two β-porphyranases and three β-agarases are analyzed by their action on defined hybrid oligosaccharides. In light of the high resolution crystal structures, the biochemical results allowed a detailed mapping of substrate specificities along the active site groove of the enzymes. Although PorA displays a strict requirement for C6-sulfate in the -2- and +1-binding subsites, PorB tolerates the presence of 3-6-anhydro-l-galactose in subsite -2. Both enzymes do not accept methylation of the galactose unit in the -1 subsite. The β-agarase AgaD requires at least four consecutive agarose units (DP8) and is highly intolerant to modifications, whereas for AgaB oligosaccharides containing C6-sulfate groups at the -4, +1, and +3 positions are still degraded. Together with a transcriptional analysis of the expression of these enzymes, the structural and biochemical results allow proposition of a model scheme for the agarolytic system of Z. galactanivorans.

PubMed: 22778272
DOI: 10.1074/JBC.M112.377184

実験手法

X-RAY DIFFRACTION (1.5 Å)