5vol: Difference between revisions

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<StructureSection load='5vol' size='340' side='right'caption='[[5vol]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
<StructureSection load='5vol' size='340' side='right'caption='[[5vol]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5vol]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VOL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VOL FirstGlance]. <br>
<table><tr><td colspan='2'>[[5vol]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_intestinalis_DSM_17393 Bacteroides intestinalis DSM 17393]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VOL 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=IPA:ISOPROPYL+ALCOHOL'>IPA</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]] 1.98&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5vol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vol OCA], [http://pdbe.org/5vol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vol RCSB], [http://www.ebi.ac.uk/pdbsum/5vol PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vol ProSAT]</span></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=IPA:ISOPROPYL+ALCOHOL'>IPA</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=5vol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vol OCA], [https://pdbe.org/5vol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vol RCSB], [https://www.ebi.ac.uk/pdbsum/5vol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vol ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/B3CET1_9BACE B3CET1_9BACE]
Arabinoxylans are constituents of the human diet. Although not utilizable by the human host, they can be fermented by colonic bacteria. The arabinoxylan backbone is decorated with arabinose side chains that may be substituted with ferulic acid, thus limiting depolymerization to fermentable sugars. We investigated the polypeptides encoded by two genes upregulated during growth of the colonic bacterium Bacteroides intestinalis on wheat arabinoxylan. The recombinant proteins, designated BiFae1A and BiFae1B, were functionally assigned esterase activities. Both enzymes were active on acetylated substrates, although each showed a higher ferulic acid esterase activity on methyl-ferulate. BiFae1A showed a catalytic efficiency of 12mM s-1 on para-nitrophenyl-acetate, and on methyl-ferulate, the value was 27 times higher. BiFae1B showed low catalytic efficiencies for both substrates. Furthermore, the two enzymes released ferulic acid from various structural elements, and NMR spectroscopy indicated complete de-esterification of arabinoxylan oligosaccharides from wheat bran. BiFae1A is a tetramer based on the crystal structure, whereas BiFae1B is a dimer in solution based on size exclusion chromatography. The structure of BiFae1A was solved to 1.98A resolution, and two tetramers were observed in the asymmetric unit. A flexible loop that may act as a hinge over the active site and likely coordinates critical interactions with the substrate was prominent in BiFae1A. Sequence alignments of the esterase domains in BiFae1B with the feruloyl esterase from Clostridium thermocellum suggest that both domains lack the flexible hinge in BiFae1A, an observation that may partly provide a molecular basis for the differences in activities in the two esterases.
 
Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides intestinalis and their Synergistic Activities with Cognate Xylanases.,Wefers D, Cavalcante JJV, Schendel RR, Deveryshetty J, Wang K, Wawrzak Z, Mackie RI, Koropatkin NM, Cann I J Mol Biol. 2017 Aug 4;429(16):2509-2527. doi: 10.1016/j.jmb.2017.06.017. Epub, 2017 Jun 29. PMID:28669823<ref>PMID:28669823</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5vol" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacteroides intestinalis DSM 17393]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cann, I]]
[[Category: Cann I]]
[[Category: Koropatkin, N M]]
[[Category: Koropatkin NM]]
[[Category: Mackie, R I]]
[[Category: Mackie RI]]
[[Category: Arabinoxylan esterase]]
[[Category: Bacteroides intestinali]]
[[Category: Carbohydrate esterase family 1]]
[[Category: Ce1]]
[[Category: Ferulic acid esterase]]
[[Category: Hydrolase]]

Latest revision as of 14:11, 13 March 2024

Bacint_04212 ferulic acid esterase

5vol, resolution 1.98Å

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