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| | ==The Structure of a family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum in complex with 1,3-linked arabinoside of xylobiose.== | | ==The Structure of a family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum in complex with 1,3-linked arabinoside of xylobiose.== |
| - | <StructureSection load='2c8n' size='340' side='right' caption='[[2c8n]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='2c8n' size='340' side='right'caption='[[2c8n]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2c8n]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"ruminiclostridium_thermocellum"_yutin_and_galperin_2013 "ruminiclostridium thermocellum" yutin and galperin 2013]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C8N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2c8n]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus Acetivibrio thermocellus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C8N FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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]] 2.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2c7f|2c7f]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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=2c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8n OCA], [https://pdbe.org/2c8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c8n RCSB], [https://www.ebi.ac.uk/pdbsum/2c8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c8n 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=2c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8n OCA], [http://pdbe.org/2c8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c8n RCSB], [http://www.ebi.ac.uk/pdbsum/2c8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2c8n ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/IABF_ACET2 IABF_ACET2] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in small oligosaccharides as alpha-(1->5)-linked arabinobiose/arabinotriose, but does not display significant activity against linear non-substituted arabinan. It is also highly efficient in the cleavage of alpha-(1->3)-linked arabinoside of xylobiose and of the alpha-(1->3)-linked arabinoside decorations of polymeric wheat arabinoxylan. It exhibits very low activity against sugar beet arabinan.<ref>PMID:16336192</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ruminiclostridium thermocellum yutin and galperin 2013]] | + | [[Category: Acetivibrio thermocellus]] |
| - | [[Category: Non-reducing end alpha-L-arabinofuranosidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Davies, G J]] | + | [[Category: D'Souza S]] |
| - | [[Category: Gilbert, H J]] | + | [[Category: Davies GJ]] |
| - | [[Category: Smith, N L]] | + | [[Category: Gilbert HJ]] |
| - | [[Category: Souza, S D]] | + | [[Category: Smith NL]] |
| - | [[Category: Taylor, E J]] | + | [[Category: Taylor EJ]] |
| - | [[Category: Turkenburg, J P]] | + | [[Category: Turkenburg JP]] |
| - | [[Category: Arabinan]]
| + | |
| - | [[Category: Arabinofuranosidase]]
| + | |
| - | [[Category: Glycosidase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Xylan]]
| + | |
| Structural highlights
Function
IABF_ACET2 Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in small oligosaccharides as alpha-(1->5)-linked arabinobiose/arabinotriose, but does not display significant activity against linear non-substituted arabinan. It is also highly efficient in the cleavage of alpha-(1->3)-linked arabinoside of xylobiose and of the alpha-(1->3)-linked arabinoside decorations of polymeric wheat arabinoxylan. It exhibits very low activity against sugar beet arabinan.[1]
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
The digestion of the plant cell wall requires the concerted action of a diverse repertoire of enzyme activities. An important component of these hydrolase consortia are arabinofuranosidases, which release L-arabinofuranose moieties from a range of plant structural polysaccharides. The anaerobic bacterium Clostridium thermocellum, a highly efficient plant cell wall degrader, possesses a single alpha-L-arabinofuranosidase (EC 3.2.1.55), CtAraf51A, located in GH51 (glycoside hydrolase family 51). The crystal structure of the enzyme has been solved in native form and in 'Michaelis' complexes with both alpha-1,5-linked arabinotriose and alpha-1,3 arabinoxylobiose, both forming a hexamer in the asymmetric unit. Kinetic studies reveal that CtAraf51A, in contrast with well-characterized GH51 enzymes including the Cellvibrio japonicus enzyme [Beylot, McKie, Voragen, Doeswijk-Voragen and Gilbert (2001) Biochem. J. 358, 607-614], catalyses the hydrolysis of alpha-1,5-linked arabino-oligosaccharides and the alpha-1,3 arabinosyl side chain decorations of xylan with equal efficiency. The paucity of direct hydrogen bonds with the aglycone moiety and the flexible conformation adopted by Trp(178), which stacks against the sugar at the +1 subsite, provide a structural explanation for the plasticity in substrate specificity displayed by the clostridial arabinofuranosidase.
Structural insight into the ligand specificity of a thermostable family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum.,Taylor EJ, Smith NL, Turkenburg JP, D'Souza S, Gilbert HJ, Davies GJ Biochem J. 2006 Apr 1;395(1):31-7. PMID:16336192[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Taylor EJ, Smith NL, Turkenburg JP, D'Souza S, Gilbert HJ, Davies GJ. Structural insight into the ligand specificity of a thermostable family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum. Biochem J. 2006 Apr 1;395(1):31-7. PMID:16336192 doi:http://dx.doi.org/10.1042/BJ20051780
- ↑ Taylor EJ, Smith NL, Turkenburg JP, D'Souza S, Gilbert HJ, Davies GJ. Structural insight into the ligand specificity of a thermostable family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum. Biochem J. 2006 Apr 1;395(1):31-7. PMID:16336192 doi:http://dx.doi.org/10.1042/BJ20051780
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