6UB4
Crystal structure (C2 form) of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose
Summary for 6UB4
| Entry DOI | 10.2210/pdb6ub4/pdb |
| Related PRD ID | PRD_900024 |
| Descriptor | GLYCOSIDE HYDROLASE, beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose, beta-D-glucopyranose-(1-3)-beta-D-glucopyranose, ... (6 entities in total) |
| Functional Keywords | glycosyl hydrolase, carbohydrate, hydrolase |
| Biological source | Lentinula edodes (Shiitake mushroom) |
| Total number of polymer chains | 2 |
| Total formula weight | 59016.83 |
| Authors | Santos, C.R.,Lima, E.A.,Mandelli, F.,Murakami, M.T. (deposition date: 2019-09-11, release date: 2020-05-20, Last modification date: 2024-10-23) |
| Primary citation | Santos, C.R.,Costa, P.A.C.R.,Vieira, P.S.,Gonzalez, S.E.T.,Correa, T.L.R.,Lima, E.A.,Mandelli, F.,Pirolla, R.A.S.,Domingues, M.N.,Cabral, L.,Martins, M.P.,Cordeiro, R.L.,Junior, A.T.,Souza, B.P.,Prates, E.T.,Gozzo, F.C.,Persinoti, G.F.,Skaf, M.S.,Murakami, M.T. Structural insights into beta-1,3-glucan cleavage by a glycoside hydrolase family. Nat.Chem.Biol., 16:920-929, 2020 Cited by PubMed Abstract: The fundamental and assorted roles of β-1,3-glucans in nature are underpinned on diverse chemistry and molecular structures, demanding sophisticated and intricate enzymatic systems for their processing. In this work, the selectivity and modes of action of a glycoside hydrolase family active on β-1,3-glucans were systematically investigated combining sequence similarity network, phylogeny, X-ray crystallography, enzyme kinetics, mutagenesis and molecular dynamics. This family exhibits a minimalist and versatile (α/β)-barrel scaffold, which can harbor distinguishing exo or endo modes of action, including an ancillary-binding site for the anchoring of triple-helical β-1,3-glucans. The substrate binding occurs via a hydrophobic knuckle complementary to the canonical curved conformation of β-1,3-glucans or through a substrate conformational change imposed by the active-site topology of some fungal enzymes. Together, these findings expand our understanding of the enzymatic arsenal of bacteria and fungi for the breakdown and modification of β-1,3-glucans, which can be exploited for biotechnological applications. PubMed: 32451508DOI: 10.1038/s41589-020-0554-5 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.6 Å) |
Structure validation
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