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Exploring molecular determinants of polysaccharide lyase family 6–1 enzyme activity
- Source :
- Glycobiology, Glycobiology, Oxford University Press (OUP), 2021, ⟨10.1093/glycob/cwab073⟩
- Publication Year :
- 2021
- Publisher :
- HAL CCSD, 2021.
-
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.
- Subjects :
- Models, Molecular
CAZy
Subfamily
[SDV]Life Sciences [q-bio]
010402 general chemistry
Crystallography, X-Ray
01 natural sciences
Biochemistry
Substrate Specificity
protein-carbohydrates recognition
03 medical and health sciences
Carbohydrate Conformation
Humans
Amino Acid Sequence
Binding site
Mode of action
030304 developmental biology
Polysaccharide-Lyases
chemistry.chemical_classification
0303 health sciences
biology
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM]
structure of alginate lyases
Substrate (chemistry)
Enzyme assay
0104 chemical sciences
Enzyme
chemistry
surface-binding site
Docking (molecular)
biology.protein
Subjects
Details
- Language :
- English
- ISSN :
- 09596658 and 14602423
- Database :
- OpenAIRE
- Journal :
- Glycobiology, Glycobiology, Oxford University Press (OUP), 2021, ⟨10.1093/glycob/cwab073⟩
- Accession number :
- edsair.doi.dedup.....d17a3c7540010134ffa9c00dca24d199