4J3V
Crystal structure of barley limit dextrinase in complex with a branched thio-linked hexasaccharide
Summary for 4J3V
| Entry DOI | 10.2210/pdb4j3v/pdb |
| Related | 4J3S 4J3T 4J3U 4J3W 4J3X |
| Related PRD ID | PRD_900010 |
| Descriptor | Limit dextrinase, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-1)-[alpha-D-glucopyranose-(1-4)]6-thio-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, ... (7 entities in total) |
| Functional Keywords | gh13 hydrolase, hydrolase |
| Biological source | Hordeum vulgare (barley) |
| Total number of polymer chains | 1 |
| Total formula weight | 102637.90 |
| Authors | Sim, L.,Windahl, M.S.,Moeller, M.S.,Henriksen, A. (deposition date: 2013-02-06, release date: 2014-02-12, Last modification date: 2023-11-08) |
| Primary citation | Moeller, M.S.,Windahl, M.S.,Sim, L.,Bjstrup, M.,Abou Hachem, M.,Hindsgaul, O.,Palcic, M.,Svensson, B.,Henriksen, A. Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase J.Mol.Biol., 427:1263-1277, 2015 Cited by PubMed Abstract: Complete hydrolytic degradation of starch requires hydrolysis of both the α-1,4- and α-1,6-glucosidic bonds in amylopectin. Limit dextrinase (LD) is the only endogenous barley enzyme capable of hydrolyzing the α-1,6-glucosidic bond during seed germination, and impaired LD activity inevitably reduces the maltose and glucose yields from starch degradation. Crystal structures of barley LD and active-site mutants with natural substrates, products and substrate analogues were sought to better understand the facets of LD-substrate interactions that confine high activity of LD to branched maltooligosaccharides. For the first time, an intact α-1,6-glucosidically linked substrate spanning the active site of a LD or pullulanase has been trapped and characterized by crystallography. The crystal structure reveals both the branch and main-chain binding sites and is used to suggest a mechanism for nucleophilicity enhancement in the active site. The substrate, product and analogue complexes were further used to outline substrate binding subsites and substrate binding restraints and to suggest a mechanism for avoidance of dual α-1,6- and α-1,4-hydrolytic activity likely to be a biological necessity during starch synthesis. PubMed: 25562209DOI: 10.1016/j.jmb.2014.12.019 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.45 Å) |
Structure validation
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