Summary for 4F13
| Entry DOI | 10.2210/pdb4f13/pdb |
| Related | 4E1Y 4F10 |
| Descriptor | Alginate lyase, 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid, beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid, ... (4 entities in total) |
| Functional Keywords | alpha barrel, polysaccharide lyase, alginate, lyase |
| Biological source | Sphingomonas |
| Total number of polymer chains | 2 |
| Total formula weight | 80712.30 |
| Authors | Mikami, B.,Ban, M.,Suzuki, S.,Yoon, H.-J.,Miyake, O.,Yamasaki, M.,Ogura, K.,Maruyama, Y.,Hashimoto, W.,Murata, K. (deposition date: 2012-05-06, release date: 2012-06-27, Last modification date: 2024-11-06) |
| Primary citation | Mikami, B.,Ban, M.,Suzuki, S.,Yoon, H.-J.,Miyake, O.,Yamasaki, M.,Ogura, K.,Maruyama, Y.,Hashimoto, W.,Murata, K. Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III Acta Crystallogr.,Sect.D, 68:1207-1216, 2012 Cited by PubMed Abstract: The structures of two mutants (H192A and Y246F) of a mannuronate-specific alginate lyase, A1-III, from Sphingomonas species A1 complexed with a tetrasaccharide substrate [4-deoxy-L-erythro-hex-4-ene-pyranosyluronate-(mannuronate)(2)-mannuronic acid] were determined by X-ray crystallography at around 2.2 Å resolution together with the apo form of the H192A mutant. The final models of the complex forms, which comprised two monomers (of 353 amino-acid residues each), 268-287 water molecules and two tetrasaccharide substrates, had R factors of around 0.17. A large conformational change occurred in the position of the lid loop (residues 64-85) in holo H192A and Y246F compared with that in apo H192A. The lid loop migrated about 14 Å from an open form to a closed form to interact with the bound tetrasaccharide and a catalytic residue. The tetrasaccharide was bound in the active cleft at subsites -3 to +1 as a substrate form in which the glycosidic linkage to be cleaved existed between subsites -1 and +1. In particular, the O(η) atom of Tyr68 in the closed lid loop forms a hydrogen bond to the side chain of a presumed catalytic residue, O(η) of Tyr246, which acts both as an acid and a base catalyst in a syn mechanism. PubMed: 22948922DOI: 10.1107/S090744491202495X PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.208 Å) |
Structure validation
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