Summary for 2Y5E
| Entry DOI | 10.2210/pdb2y5e/pdb |
| Related | 2Y4S |
| Related PRD ID | PRD_900015 |
| Descriptor | LIMIT DEXTRINASE, Cyclohexakis-(1-4)-(alpha-D-glucopyranose), GLYCEROL, ... (6 entities in total) |
| Functional Keywords | hydrolase, starch, pullulanase, debranching enzyme, glycoside hydrolase 13 |
| Biological source | HORDEUM VULGARE (BARLEY) |
| Total number of polymer chains | 1 |
| Total formula weight | 99622.50 |
| Authors | Vester-Christensen, M.B.,Hachem, M.A.,Svensson, B.,Henriksen, A. (deposition date: 2011-01-13, release date: 2011-01-26, Last modification date: 2023-12-20) |
| Primary citation | Vester-Christensen, M.B.,Abou Hachem, M.,Svensson, B.,Henriksen, A. Crystal Structure of an Essential Enzyme in Seed Starch Degradation: Barley Limit Dextrinase in Complex with Cyclodextrins. J.Mol.Biol., 403:739-, 2010 Cited by PubMed Abstract: Barley limit dextrinase [Hordeum vulgare limit dextrinase (HvLD)] catalyzes the hydrolysis of α-1,6 glucosidic linkages in limit dextrins. This activity plays a role in starch degradation during germination and presumably in starch biosynthesis during grain filling. The crystal structures of HvLD in complex with the competitive inhibitors α-cyclodextrin (CD) and β-CD are solved and refined to 2.5 Å and 2.1 Å, respectively, and are the first structures of a limit dextrinase. HvLD belongs to glycoside hydrolase 13 family and is composed of four domains: an immunoglobulin-like N-terminal eight-stranded β-sandwich domain, a six-stranded β-sandwich domain belonging to the carbohydrate binding module 48 family, a catalytic (β/α)(8)-like barrel domain that lacks α-helix 5, and a C-terminal eight-stranded β-sandwich domain of unknown function. The CDs are bound at the active site occupying carbohydrate binding subsites +1 and +2. A glycerol and three water molecules mimic a glucose residue at subsite -1, thereby identifying residues involved in catalysis. The bulky Met440, a unique residue at its position among α-1,6 acting enzymes, obstructs subsite -4. The steric hindrance observed is proposed to affect substrate specificity and to cause a low activity of HvLD towards amylopectin. An extended loop (Asp513-Asn520) between β5 and β6 of the catalytic domain also seems to influence substrate specificity and to give HvLD a higher affinity for α-CD than pullulanases. The crystal structures additionally provide new insight into cation sites and the concerted action of the battery of hydrolytic enzymes in starch degradation. PubMed: 20863834DOI: 10.1016/J.JMB.2010.09.031 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.49 Å) |
Structure validation
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