1wd4
From Proteopedia
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|PDB= 1wd4 |SIZE=350|CAPTION= <scene name='initialview01'>1wd4</scene>, resolution 2.07Å | |PDB= 1wd4 |SIZE=350|CAPTION= <scene name='initialview01'>1wd4</scene>, resolution 2.07Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene> | + | |LIGAND= <scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Alpha-N-arabinofuranosidase Alpha-N-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-N-arabinofuranosidase Alpha-N-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1wd3|1WD3]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wd4 OCA], [http://www.ebi.ac.uk/pdbsum/1wd4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wd4 RCSB]</span> | ||
}} | }} | ||
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[[Category: Shoun, H.]] | [[Category: Shoun, H.]] | ||
[[Category: Wakagi, T.]] | [[Category: Wakagi, T.]] | ||
| - | [[Category: AHR]] | ||
[[Category: beta-sandwich]] | [[Category: beta-sandwich]] | ||
[[Category: beta-trefoil]] | [[Category: beta-trefoil]] | ||
[[Category: complex with arabinose]] | [[Category: complex with arabinose]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:34:36 2008'' |
Revision as of 21:34, 30 March 2008
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| , resolution 2.07Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | Alpha-N-arabinofuranosidase, with EC number 3.2.1.55 | ||||||
| Related: | 1WD3
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of arabinofuranosidase complexed with arabinose
Overview
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.
About this Structure
1WD4 is a Single protein structure of sequence from Aspergillus kawachii. Full crystallographic information is available from OCA.
Reference
Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose., Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S, J Biol Chem. 2004 Oct 22;279(43):44907-14. Epub 2004 Aug 3. PMID:15292273
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