View source for 9fz2


==Crystal structure of Amylase 5 (Amy5) from Ruminococcus bromii covalently bound to alpha-1,6 branched pseudo-trisaccharide activity-based probe==
<StructureSection load='9fz2' size='340' side='right'caption='[[9fz2]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9fz2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruminococcus_bromii Ruminococcus bromii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9FZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9FZ2 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]] 1.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1IHI:8-azanyloctan-1-ol'>A1IHI</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PBW:(1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol'>PBW</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=9fz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9fz2 OCA], [https://pdbe.org/9fz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9fz2 RCSB], [https://www.ebi.ac.uk/pdbsum/9fz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9fz2 ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
alpha-Amylases are the workhorse enzymes of starch degradation. They are central to human health, including as targets for anti-diabetic compounds, but are also the key enzymes in the industrial processing of starch for biofuels, corn syrups, brewing and detergents. Dissection of the activity, specificity and stability of alpha-amylases is crucial to understanding their biology and allowing their exploitation. Yet, functional characterization lags behind DNA sequencing and genomics; and new tools are required for rapid analysis of alpha-amylase function. Here, we design, synthesize and apply new branched alpha-amylase activity-based probes. Using both alpha-1,6 branched and unbranched alpha-1,4 maltobiose activity-based probes we were able to explore the stability and substrate specificity of both a panel of human gut microbial alpha-amylases and a panel of industrially relevant alpha-amylases. We also demonstrate how we can detect and annotate the substrate specificity of alpha-amylases in the complex cell lysate of both a prominent gut microbe and a diverse compost sample by in-gel fluorescence and mass spectrometry. A toolbox of starch-active activity-based probes will enable rapid functional dissection of alpha-amylases. We envisage activity-based probes contributing to better selection and engineering of enzymes for industrial application as well as fundamental analysis of enzymes in human health.

Precision Activity-Based alpha-Amylase Probes for Dissection and Annotation of Linear and Branched-Chain Starch-Degrading Enzymes.,Pickles IB, Chen Y, Moroz O, Brown HA, de Boer C, Armstrong Z, McGregor NGS, Artola M, Codee JDC, Koropatkin NM, Overkleeft HS, Davies GJ Angew Chem Int Ed Engl. 2024 Nov 27:e202415219. doi: 10.1002/anie.202415219. PMID:39601378<ref>PMID:39601378</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 9fz2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Ruminococcus bromii]]
[[Category: Davies G]]
[[Category: Moroz O]]
[[Category: Pickles IB]]