7O79

Structure of the PL6 family polysaccharide lyase Pedsa3628 from Pseudopedobacter saltans

7O79 の概要

• エントリーDOI: 10.2210/pdb7o79/pdb
• 分子名称: Poly(Beta-D-mannuronate) lyase, PHOSPHATE ION (3 entities in total)
• 機能のキーワード: beta helix, polysaccharide lyase, lyase
• 由来する生物種: Pseudopedobacter saltans (strain ATCC 51119 / DSM 12145 / JCM 21818 / LMG 10337 / NBRC 100064 / NCIMB 13643) (Pedobacter saltans)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 50073.17

構造登録者

Ballut, L.,Violot, S.,Carrique, L.,Aghajari, N. (登録日: 2021-04-13, 公開日: 2021-07-28, 最終更新日: 2024-01-31)

主引用文献

Violot, S.,Galisson, F.,Carrique, L.,Jugnarain, V.,Conchou, L.,Robert, X.,Thureau, A.,Helbert, W.,Aghajari, N.,Ballut, L.
Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity.
Glycobiology, 31:1557-1570, 2021

PubMed Abstract: The polysaccharide lyase family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exolyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirms that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform that can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel β-helix fold shared by all these enzymes, the substrate-binding site harbors the same overall conserved structures and organization. Despite this apparent similarity, it appears that members of the PL6_1 subfamily specifically accommodate and catalyze the degradation of different alginates suggesting that this common platform is actually a highly adaptable and specific tool.

PubMed: 34245266
DOI: 10.1093/glycob/cwab073

実験手法

X-RAY DIFFRACTION (1.93 Å)