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| | ==Structure of CBM35 in complex with glucuronic acid== | | ==Structure of CBM35 in complex with glucuronic acid== |
| - | <StructureSection load='4qb2' size='340' side='right' caption='[[4qb2]], [[Resolution|resolution]] 1.50Å' scene=''> | + | <StructureSection load='4qb2' size='340' side='right'caption='[[4qb2]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4qb2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp._bp-23 Bacillus sp. bp-23]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QB2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4qb2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_barcinonensis Paenibacillus barcinonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QB2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BDP:BETA-D-GLUCOPYRANURONIC+ACID'>BDP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BDP:BETA-D-GLUCOPYRANURONIC+ACID'>BDP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qaw|4qaw]], [[4qb1|4qb1]], [[4qb6|4qb6]]</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=4qb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qb2 OCA], [https://pdbe.org/4qb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qb2 RCSB], [https://www.ebi.ac.uk/pdbsum/4qb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qb2 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xyn30d ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198119 Bacillus sp. BP-23])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>
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| - | <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=4qb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qb2 OCA], [http://pdbe.org/4qb2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qb2 RCSB], [http://www.ebi.ac.uk/pdbsum/4qb2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qb2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/H6WCZ0_PAEBA H6WCZ0_PAEBA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus sp. bp-23]] | + | [[Category: Large Structures]] |
| - | [[Category: Endo-1,4-beta-xylanase]] | + | [[Category: Paenibacillus barcinonensis]] |
| - | [[Category: Sainz-Polo, M A]] | + | [[Category: Sainz-Polo MA]] |
| - | [[Category: Sanz-Aparicio, J]] | + | [[Category: Sanz-Aparicio J]] |
| - | [[Category: Beta-structure]]
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| - | [[Category: Calcium binding]]
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| - | [[Category: Carbohydrate binding module]]
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| - | [[Category: Cell wall]]
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| - | [[Category: Sugar binding protein]]
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| Structural highlights
Function
H6WCZ0_PAEBA
Publication Abstract from PubMed
Glucuronoxylanase Xyn30D is a modular enzyme containing a family 30 glycoside hydrolase catalytic domain and an attached carbohydrate binding module of the CBM35 family. We present here the three-dimensional structure of the full-length Xyn30D at 2.4 A resolution. The catalytic domain folds into an (alpha/beta)8 barrel with an associated beta-structure, while the attached CBM35 displays a jellyroll beta-sandwich including two calcium ions. Although both domains fold in an independent manner, the linker region makes polar interactions with the catalytic domain allowing a moderate flexibility. The ancillary Xyn30D-CBM35 domain has been expressed and crystallized and its binding abilities have been investigated by soaking experiments. Only glucuronic acid-containing ligands produced complexes, and their structures have been solved. A calcium dependent glucuronic acid binding site shows distinctive structural features as compared to other uronic acid specific CBM35s, as the presence of two aromatic residues delineating a wider pocket. The non-conserved Glu129 makes a bidentate link to calcium and defines region E, previously identified as specificity hot spot. The molecular surface of Xyn30D-CBM35 shows a unique stretch of negative charge distribution extending from its binding pocket that might indicate some oriented interaction with its target substrate. The binding ability of Xyn30D-CBM35 to different xylans was analyzed by affinity gel electrophoresis. Some binding was observed with rye glucuronoarabinoxylan in presence of calcium chelating EDTA, which would indicate that Xyn30D-CBM35 might establish interaction to other components of xylan, such as arabinose decorations of glucuronoarabinoxylan. A role in depolymerization of highly substituted chemically complex xylans is proposed.
Structural analysis of glucuronoxylan specific Xyn30D and its attached CBM35 domain give insights into the role of modularity in specificity.,Sainz-Polo MA, Valenzuela SV, Gonzalez B, Pastor FI, Sanz-Aparicio J J Biol Chem. 2014 Sep 8. pii: jbc.M114.597732. PMID:25202007[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sainz-Polo MA, Valenzuela SV, Gonzalez B, Pastor FI, Sanz-Aparicio J. Structural analysis of glucuronoxylan specific Xyn30D and its attached CBM35 domain give insights into the role of modularity in specificity. J Biol Chem. 2014 Sep 8. pii: jbc.M114.597732. PMID:25202007 doi:http://dx.doi.org/10.1074/jbc.M114.597732
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