1wd4
From Proteopedia
(New page: 200px<br /><applet load="1wd4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wd4, resolution 2.07Å" /> '''Crystal structure of...) |
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| - | [[Image:1wd4.jpg|left|200px]]<br /><applet load="1wd4" size=" | + | [[Image:1wd4.jpg|left|200px]]<br /><applet load="1wd4" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1wd4, resolution 2.07Å" /> | caption="1wd4, resolution 2.07Å" /> | ||
'''Crystal structure of arabinofuranosidase complexed with arabinose'''<br /> | '''Crystal structure of arabinofuranosidase complexed with arabinose'''<br /> | ||
==Overview== | ==Overview== | ||
| - | As the first known structures of a glycoside hydrolase family 54 (GH54) | + | 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== | ==About this Structure== | ||
| - | 1WD4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_kawachii Aspergillus kawachii] with AHR as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http:// | + | 1WD4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_kawachii Aspergillus kawachii] with <scene name='pdbligand=AHR:'>AHR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WD4 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: complex with arabinose]] | [[Category: complex with arabinose]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:42:59 2008'' |
Revision as of 13:43, 21 February 2008
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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 with as ligand. Active as Alpha-N-arabinofuranosidase, with EC number 3.2.1.55 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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