8KHV
The crystal structure of glycosaminoglycan lyase GAGase II
Summary for 8KHV
| Entry DOI | 10.2210/pdb8khv/pdb |
| Descriptor | Heparinase II/III-like protein, MANGANESE (II) ION, CALCIUM ION, ... (4 entities in total) |
| Functional Keywords | glycosaminoglycan, lyase, pl_35 |
| Biological source | Spirosoma fluviale |
| Total number of polymer chains | 1 |
| Total formula weight | 68630.52 |
| Authors | |
| Primary citation | Wei, L.,Cao, H.Y.,Zou, R.,Du, M.,Zhang, Q.,Lu, D.,Xu, X.,Xu, Y.,Wang, W.,Chen, X.L.,Zhang, Y.Z.,Li, F. Crystal structure and catalytic mechanism of PL35 family glycosaminoglycan lyases with an ultrabroad substrate spectrum. Elife, 13:-, 2025 Cited by PubMed Abstract: Recently, a new class of glycosaminoglycan (GAG) lyases (GAGases) belonging to PL35 family has been discovered with an ultrabroad substrate spectrum that can degrade three types of uronic acid-containing GAGs (hyaluronic acid, chondroitin sulfate and heparan sulfate) or even alginate. In this study, the structures of GAGase II from and GAGase VII from DSM 17393 were determined at 1.9 and 2.4 Å resolution, respectively, and their catalytic mechanism was investigated by the site-directed mutant of their crucial residues and molecular docking assay. Structural analysis showed that GAGase II and GAGase VII consist of an N-terminal (α/α) toroid multidomain and a C-terminal two-layered β-sheet domain with Mn. Notably, although GAGases share similar folds and catalytic mechanisms with some GAG lyases and alginate lyases, they exhibit higher structural similarity with alginate lyases than GAG lyases, which may present a crucial structural evidence for the speculation that GAG lyases with (α/α) toroid and antiparallel β-sheet structures arrived by a divergent evolution from alginate lyases with the same folds. Overall, this study not only solved the structure of PL35 GAG lyases for the first time and investigated their catalytic mechanism, especially the reason why GAGase III can additionally degrade alginate, but also provided a key clue in the divergent evolution of GAG lyases that originated from alginate lyases. PubMed: 40387079DOI: 10.7554/eLife.102422 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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