7O79
Structure of the PL6 family polysaccharide lyase Pedsa3628 from Pseudopedobacter saltans
Summary for 7O79
| Entry DOI | 10.2210/pdb7o79/pdb |
| Descriptor | Poly(Beta-D-mannuronate) lyase, PHOSPHATE ION (3 entities in total) |
| Functional Keywords | beta helix, polysaccharide lyase, lyase |
| Biological source | Pseudopedobacter saltans (strain ATCC 51119 / DSM 12145 / JCM 21818 / LMG 10337 / NBRC 100064 / NCIMB 13643) (Pedobacter saltans) |
| Total number of polymer chains | 1 |
| Total formula weight | 50073.17 |
| Authors | Ballut, L.,Violot, S.,Carrique, L.,Aghajari, N. (deposition date: 2021-04-13, release date: 2021-07-28, Last modification date: 2024-01-31) |
| Primary citation | 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 Cited by 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: 34245266DOI: 10.1093/glycob/cwab073 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.93 Å) |
Structure validation
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