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| | <StructureSection load='3d5z' size='340' side='right'caption='[[3d5z]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='3d5z' size='340' side='right'caption='[[3d5z]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3d5z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D5Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3d5z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D5Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3cu9|3cu9]], [[3d5y|3d5y]], [[3d60|3d60]], [[3d61|3d61]]</div></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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">abn ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Arabinan_endo-1,5-alpha-L-arabinosidase Arabinan endo-1,5-alpha-L-arabinosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.99 3.2.1.99] </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=3d5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d5z OCA], [https://pdbe.org/3d5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d5z RCSB], [https://www.ebi.ac.uk/pdbsum/3d5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d5z ProSAT]</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=3d5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d5z OCA], [https://pdbe.org/3d5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d5z RCSB], [https://www.ebi.ac.uk/pdbsum/3d5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d5z ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/IABN_GEOSE IABN_GEOSE]] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of debranched arabinan, linear arabinan and short arabino-oligosaccharides (degree of polymerization from 2 to 8). It exhibits marginal activity toward sugar beet arabinan.<ref>PMID:19505290</ref>
| + | [https://www.uniprot.org/uniprot/IABN_GEOSE IABN_GEOSE] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of debranched arabinan, linear arabinan and short arabino-oligosaccharides (degree of polymerization from 2 to 8). It exhibits marginal activity toward sugar beet arabinan.<ref>PMID:19505290</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: Arabinan endo-1,5-alpha-L-arabinosidase]] | |
| - | [[Category: Atcc 12980]] | |
| - | [[Category: Large Structures]] | |
| - | [[Category: Alhassid, A]] | |
| - | [[Category: David, A Ben]] | |
| - | [[Category: Shoham, G]] | |
| - | [[Category: Shoham, Y]] | |
| - | [[Category: Arabinanase]] | |
| - | [[Category: Beta-propeller]] | |
| | [[Category: Geobacillus stearothermophilus]] | | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: Glycosyl hydrolase]] | + | [[Category: Large Structures]] |
| - | [[Category: Hydrolase]] | + | [[Category: Alhassid A]] |
| | + | [[Category: Ben David A]] |
| | + | [[Category: Shoham G]] |
| | + | [[Category: Shoham Y]] |
| Structural highlights
Function
IABN_GEOSE Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of debranched arabinan, linear arabinan and short arabino-oligosaccharides (degree of polymerization from 2 to 8). It exhibits marginal activity toward 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
Arabinanases are glycosidases that hydrolyse alpha-(1-->5)- arabinofuranosidic linkages found in the backbone of the pectic polysaccharide arabinan. Here we describe the biochemical characterization and the enzyme-substrate crystal structure of an inverting family 43 arabinanase from Geobacillus stearothermophilus T-6 (AbnB). Based on viscosity and reducing power measurements, and based on product analysis for the hydrolysis of linear arabinan by AbnB, the enzyme works in an endo mode of action. Isothermal titration calorimetry studies of a catalytic mutant with various arabino-oligosaccharides suggested that the enzyme active site can accommodate at least five arabinose units. The crystal structure of AbnB was determined at 1.06 A (1 A=0.1 nm) resolution, revealing a single five-bladed-beta-propeller fold domain. Co-crystallization of catalytic mutants of the enzyme with different substrates allowed us to obtain complex structures of AbnBE201A with arabinotriose and AbnBD147A with arabinobiose. Based on the crystal structures of AbnB together with its substrates, the position of the three catalytic carboxylates: Asp27, the general base; Glu201, the general acid; and Asp147, the pKa modulator, is in agreement with their putative catalytic roles. In the complex structure of AbnBE201A with arabinotriose, a single water molecule is located 2.8 A from Asp27 and 3.7 A from the anomeric carbon. The position of this water molecule is kept via hydrogen bonding with a conserved tyrosine (Tyr229) that is 2.6 A distant from it. The location of this molecule suggests that it can function as the catalytic water molecule in the hydrolysis reaction, resulting in the inversion of the anomeric configuration of the product.
Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate.,Alhassid A, Ben-David A, Tabachnikov O, Libster D, Naveh E, Zolotnitsky G, Shoham Y, Shoham G Biochem J. 2009 Jul 29;422(1):73-82. PMID:19505290[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Alhassid A, Ben-David A, Tabachnikov O, Libster D, Naveh E, Zolotnitsky G, Shoham Y, Shoham G. Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate. Biochem J. 2009 Jul 29;422(1):73-82. PMID:19505290 doi:10.1042/BJ20090180
- ↑ Alhassid A, Ben-David A, Tabachnikov O, Libster D, Naveh E, Zolotnitsky G, Shoham Y, Shoham G. Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate. Biochem J. 2009 Jul 29;422(1):73-82. PMID:19505290 doi:10.1042/BJ20090180
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