4qb2: Difference between revisions
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==Structure of CBM35 in complex with glucuronic acid== | |||
<StructureSection load='4qb2' size='340' side='right'caption='[[4qb2]], [[Resolution|resolution]] 1.50Å' scene=''> | |||
== Structural highlights == | |||
<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</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='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> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/H6WCZ0_PAEBA H6WCZ0_PAEBA] | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:25202007</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4qb2" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Paenibacillus barcinonensis]] | |||
[[Category: Sainz-Polo MA]] | |||
[[Category: Sanz-Aparicio J]] | |||
