1WD4

Crystal structure of arabinofuranosidase complexed with arabinose

1WD4 の概要

• エントリーDOI: 10.2210/pdb1wd4/pdb
• 関連するPDBエントリー: 1WD3
• 分子名称: alpha-L-arabinofuranosidase B, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-L-arabinofuranose, ... (4 entities in total)
• 機能のキーワード: beta-sandwich, beta-trefoil, complex with arabinose, hydrolase
• 由来する生物種: Aspergillus kawachii
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 51758.33

構造登録者

Miyanaga, A.,Koseki, T.,Matsuzawa, H.,Wakagi, T.,Shoun, H.,Fushinobu, S. (登録日: 2004-05-11, 公開日: 2004-09-14, 最終更新日: 2024-11-20)

主引用文献

Miyanaga, A.,Koseki, T.,Matsuzawa, H.,Wakagi, T.,Shoun, H.,Fushinobu, S.
Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose
J.Biol.Chem., 279:44907-44914, 2004

PubMed Abstract: As the first known structures of a glycoside hydrolase family 54 (GH54) enzyme, we determined the crystal structures of free and arabinose-complex forms of Aspergillus kawachii IFO4308 alpha-l-arabinofuranosidase (AkAbfB). AkAbfB comprises two domains: a catalytic domain and an arabinose-binding domain (ABD). The catalytic domain has a beta-sandwich fold similar to those of clan-B glycoside hydrolases. ABD has a beta-trefoil fold similar to that of carbohydrate-binding module (CBM) family 13. However, ABD shows a number of characteristics distinctive from those of CBM family 13, suggesting that it could be classified into a new CBM family. In the arabinose-complex structure, one of three arabinofuranose molecules is bound to the catalytic domain through many interactions. Interestingly, a disulfide bond formed between two adjacent cysteine residues recognized the arabinofuranose molecule in the active site. From the location of this arabinofuranose and the results of a mutational study, the nucleophile and acid/base residues were determined to be Glu(221) and Asp(297), respectively. The other two arabinofuranose molecules are bound to ABD. The O-1 atoms of the two arabinofuranose molecules bound at ABD are both pointed toward the solvent, indicating that these sites can both accommodate an arabinofuranose side-chain moiety linked to decorated arabinoxylans.

PubMed: 15292273
DOI: 10.1074/jbc.M405390200

実験手法

X-RAY DIFFRACTION (2.07 Å)