6UB1

Crystal structure of a GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii (BgGH128_III) in complex with laminaribiose at -3 and -2 subsites

Summary for 6UB1

• Entry DOI: 10.2210/pdb6ub1/pdb
• Related PRD ID: PRD_900024
• Descriptor: GLYCOSIDE HYDROLASE, beta-D-glucopyranose-(1-3)-beta-D-glucopyranose, beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: glycosyl hydrolase, carbohydrate, hydrolase
• Biological source: Blastomyces gilchristii
• Total number of polymer chains: 4
• Total formula weight: 113179.59

Authors

Costa, P.A.C.R.,Santos, C.R.,Domingues, M.N.,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

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: 32451508
DOI: 10.1038/s41589-020-0554-5

Experimental method

X-RAY DIFFRACTION (1.6 Å)