1WD3
Crystal structure of arabinofuranosidase
Summary for 1WD3
| Entry DOI | 10.2210/pdb1wd3/pdb |
| Related | 1WD4 |
| Descriptor | alpha-L-arabinofuranosidase B, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total) |
| Functional Keywords | beta-sandwich, beta-trefoil, hydrolase |
| Biological source | Aspergillus kawachii |
| Total number of polymer chains | 1 |
| Total formula weight | 51307.94 |
| Authors | Miyanaga, A.,Koseki, T.,Matsuzawa, H.,Wakagi, T.,Shoun, H.,Fushinobu, S. (deposition date: 2004-05-11, release date: 2004-09-14, Last modification date: 2024-10-16) |
| Primary citation | 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 Cited by 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: 15292273DOI: 10.1074/jbc.M405390200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.75 Å) |
Structure validation
Download full validation report
