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| | ==Crystal structure of arabinofuranosidase== | | ==Crystal structure of arabinofuranosidase== |
| - | <StructureSection load='1wd3' size='340' side='right' caption='[[1wd3]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='1wd3' size='340' side='right'caption='[[1wd3]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1wd3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspka Aspka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WD3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WD3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1wd3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_luchuensis Aspergillus luchuensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WD3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wd4|1wd4]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wd3 OCA], [https://pdbe.org/1wd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1wd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wd3 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wd3 OCA], [http://pdbe.org/1wd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1wd3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wd3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ABFB_ASPKW ABFB_ASPKW] Alpha-L-arabinofuranosidase involved in the degradation of arabinoxylan, a major component of plant hemicellulose. Able to hydrolyze 1,5-, 1,3- and 1,2-alpha-linkages not only in L-arabinofuranosyl oligosaccharides, but also in polysaccharides containing terminal non-reducing L-arabinofuranoses in side chains, like L-arabinan, arabinogalactan and arabinoxylan.<ref>PMID:15292273</ref> <ref>PMID:16233515</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wd/1wd3_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wd/1wd3_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aspka]] | + | [[Category: Aspergillus luchuensis]] |
| - | [[Category: Non-reducing end alpha-L-arabinofuranosidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Fushinobu, S]] | + | [[Category: Fushinobu S]] |
| - | [[Category: Koseki, T]] | + | [[Category: Koseki T]] |
| - | [[Category: Matsuzawa, H]] | + | [[Category: Matsuzawa H]] |
| - | [[Category: Miyanaga, A]] | + | [[Category: Miyanaga A]] |
| - | [[Category: Shoun, H]] | + | [[Category: Shoun H]] |
| - | [[Category: Wakagi, T]] | + | [[Category: Wakagi T]] |
| - | [[Category: Beta-sandwich]]
| + | |
| - | [[Category: Beta-trefoil]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
ABFB_ASPKW Alpha-L-arabinofuranosidase involved in the degradation of arabinoxylan, a major component of plant hemicellulose. Able to hydrolyze 1,5-, 1,3- and 1,2-alpha-linkages not only in L-arabinofuranosyl oligosaccharides, but also in polysaccharides containing terminal non-reducing L-arabinofuranoses in side chains, like L-arabinan, arabinogalactan and arabinoxylan.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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. 2004 Oct 22;279(43):44907-14. Epub 2004 Aug 3. PMID:15292273 doi:10.1074/jbc.M405390200
- ↑ Koseki T, Okuda M, Sudoh S, Kizaki Y, Iwano K, Aramaki I, Matsuzawa H. Role of two alpha-L-arabinofuranosidases in arabinoxylan degradation and characteristics of the encoding genes from shochu koji molds, Aspergillus kawachii and Aspergillus awamori. J Biosci Bioeng. 2003;96(3):232-41. doi: 10.1016/s1389-1723(03)80187-1. PMID:16233515 doi:http://dx.doi.org/10.1016/s1389-1723(03)80187-1
- ↑ 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. 2004 Oct 22;279(43):44907-14. Epub 2004 Aug 3. PMID:15292273 doi:10.1074/jbc.M405390200
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