6JPN

Crystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila

Summary for 6JPN

• Entry DOI: 10.2210/pdb6jpn/pdb
• Related: 6JP4
• Descriptor: Alginate lyase, beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid, MANGANESE (II) ION, ... (6 entities in total)
• Functional Keywords: alpha barrel+beta sandwich, lyase
• Biological source: Defluviitalea phaphyphila
• Total number of polymer chains: 1
• Total formula weight: 89428.84

Authors

Ji, S.Q.,Dix, S.R.,Aziz, A.,Sedelnikova, S.E.,Li, F.L.,Rice, D.W. (deposition date: 2019-03-27, release date: 2019-10-30, Last modification date: 2024-03-27)

Primary citation

Ji, S.,Dix, S.R.,Aziz, A.A.,Sedelnikova, S.E.,Baker, P.J.,Rafferty, J.B.,Bullough, P.A.,Tzokov, S.B.,Agirre, J.,Li, F.L.,Rice, D.W.
The molecular basis of endolytic activity of a multidomain alginate lyase fromDefluviitalea phaphyphila, a representative of a new lyase family, PL39.
J.Biol.Chem., 294:18077-18091, 2019

PubMed Abstract: Alginate is a polymer containing two uronic acid epimers, β-d-mannuronate (M) and α-l-guluronate (G), and is a major component of brown seaweed that is depolymerized by alginate lyases. These enzymes have diverse specificity, cleaving the chain with endo- or exotype activity and with differential selectivity for the sequence of M or G at the cleavage site. Dp0100 is a 201-kDa multimodular, broad-specificity endotype alginate lyase from the marine thermophile , which uses brown algae as a carbon source, converting it to ethanol, and bioinformatics analysis suggested that its catalytic domain represents a new polysaccharide lyase family, PL39. The structure of the Dp0100 catalytic domain, determined at 2.07 Å resolution, revealed that it comprises three regions strongly resembling those of the exotype lyase families PL15 and PL17. The conservation of key catalytic histidine and tyrosine residues belonging to the latter suggests these enzymes share mechanistic similarities. A complex of Dp0100 with a pentasaccharide, M, showed that the oligosaccharide is located in subsites -2, -1, +1, +2, and +3 in a long, deep canyon open at both ends, explaining the endotype activity of this lyase. This contrasted with the hindered binding sites of the exotype enzymes, which are blocked such that only one sugar moiety can be accommodated at the -1 position in the catalytic site. The biochemical and structural analyses of Dp0100, the first for this new class of endotype alginate lyases, have furthered our understanding of the structure-function and evolutionary relationships within this important class of enzymes.

PubMed: 31624143
DOI: 10.1074/jbc.RA119.010716

Experimental method

X-RAY DIFFRACTION (2.85 Å)