3AFL
Crystal structure of exotype alginate lyase Atu3025 H531A complexed with alginate trisaccharide
Summary for 3AFL
| Entry DOI | 10.2210/pdb3afl/pdb |
| Related | 3A0O |
| Descriptor | Oligo alginate lyase, 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid (3 entities in total) |
| Functional Keywords | alpha/alpha ballel, anti-parallel beta sheet, lyase |
| Biological source | Agrobacterium tumefaciens |
| Total number of polymer chains | 1 |
| Total formula weight | 88433.26 |
| Authors | Ochiai, A.,Yamasaki, M.,Mikami, B.,Hashimoto, W.,Murata, K. (deposition date: 2010-03-09, release date: 2010-04-28, Last modification date: 2023-11-01) |
| Primary citation | Ochiai, A.,Yamasaki, M.,Mikami, B.,Hashimoto, W.,Murata, K. Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens J.Biol.Chem., 285:24519-24528, 2010 Cited by PubMed Abstract: Alginate, a major component of the cell wall matrix in brown seaweeds, is degraded by alginate lyases through a beta-elimination reaction. Almost all alginate lyases act endolytically on substrate, thereby yielding unsaturated oligouronic acids having 4-deoxy-l-erythro-hex-4-enepyranosyluronic acid at the nonreducing end. In contrast, Agrobacterium tumefaciens alginate lyase Atu3025, a member of polysaccharide lyase family 15, acts on alginate polysaccharides and oligosaccharides exolytically and releases unsaturated monosaccharides from the substrate terminal. The crystal structures of Atu3025 and its inactive mutant in complex with alginate trisaccharide (H531A/DeltaGGG) were determined at 2.10- and 2.99-A resolutions with final R-factors of 18.3 and 19.9%, respectively, by x-ray crystallography. The enzyme is comprised of an alpha/alpha-barrel + anti-parallel beta-sheet as a basic scaffold, and its structural fold has not been seen in alginate lyases analyzed thus far. The structural analysis of H531A/DeltaGGG and subsequent site-directed mutagenesis studies proposed the enzyme reaction mechanism, with His(311) and Tyr(365) as the catalytic base and acid, respectively. Two structural determinants, i.e. a short alpha-helix in the central alpha/alpha-barrel domain and a conformational change at the interface between the central and C-terminal domains, are essential for the exolytic mode of action. This is, to our knowledge, the first report on the structure of the family 15 enzyme. PubMed: 20507980DOI: 10.1074/jbc.M110.125450 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.99 Å) |
Structure validation
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