2Y5E

BARLEY LIMIT DEXTRINASE IN COMPLEX WITH ALPHA-CYCLODEXTRIN

「2X4C」から置き換えられました

2Y5E の概要

• エントリーDOI: 10.2210/pdb2y5e/pdb
• 関連するPDBエントリー: 2Y4S
• 関連するBIRD辞書のPRD_ID: PRD_900015
• 分子名称: LIMIT DEXTRINASE, Cyclohexakis-(1-4)-(alpha-D-glucopyranose), GLYCEROL, ... (6 entities in total)
• 機能のキーワード: hydrolase, starch, pullulanase, debranching enzyme, glycoside hydrolase 13
• 由来する生物種: HORDEUM VULGARE (BARLEY)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 99622.50

構造登録者

Vester-Christensen, M.B.,Hachem, M.A.,Svensson, B.,Henriksen, A. (登録日: 2011-01-13, 公開日: 2011-01-26, 最終更新日: 2023-12-20)

主引用文献

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

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: 20863834
DOI: 10.1016/J.JMB.2010.09.031

実験手法

X-RAY DIFFRACTION (2.49 Å)