3qed: Difference between revisions
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The | ==The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases== | ||
<StructureSection load='3qed' size='340' side='right'caption='[[3qed]], [[Resolution|resolution]] 2.99Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3qed]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus_Ueda107 Cellvibrio japonicus Ueda107]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QED 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]] 2.99Å</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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</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=3qed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qed OCA], [https://pdbe.org/3qed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qed RCSB], [https://www.ebi.ac.uk/pdbsum/3qed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qed ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/B3PD60_CELJU B3PD60_CELJU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Reflecting the diverse chemistry of plant cell walls, microorganisms that degrade these composite structures synthesize an array of glycoside hydrolases. These enzymes are organized into sequence-, mechanism- and structure-based families. Genomic data has shown that several organisms that degrade the plant cell wall contain a large number of genes encoding family 43 (GH43) glycoside hydrolases. Here we report the biochemical properties of the GH43 enzymes of a saprophytic soil bacterium, Cellvibrio japonicus, and a human colonic symbiont, Bacteroides thetaiotaomicron. The data show that C. japonicus uses predominantly exo-acting enzymes to degrade arabinan into arabinose, while B. thetaiotaomicron deploys a combination of endo and side chain-cleaving glycoside hydrolases. Both organisms, however, utilize an arabinan-specific alpha-1,2-arabinofuranosidase in the degradative process, an activity that has not previously been reported. The enzyme can cleave alpha-1,2-arabinofuranose decorations in single or double substitutions, the latter being recalcitrant to the action of other arabinofuranosidases. The crystal structure of the C. japonicus arabinan-specific alpha-1,2-arabinofuranosidase, CjAbf43A displays a 5-bladed beta-propeller fold. The specificity of the enzyme for arabinan is conferred by a surface cleft that is complementary to the helical backbone of the polysaccharide. The specificity of CjAbf43A for alpha-1,2-L-arabinofuranose side chains is conferred by a polar residue that orientates the arabinan backbone such that O2 arabinose decorations are directed into the active site pocket. A shelf-like structure adjacent to the active site pocket accommodates O3 arabinose side chains, explaining how the enzyme can target O2 linkages that are components of single or double substitutions. | |||
The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases.,Cartmell A, McKee L, Pena MJ, Larsbrink J, Brumer H, Kaneko S, Ichinose H, Lewis RJ, Vikso-Nielsen A, Gilbert HJ, Marles-Wright J J Biol Chem. 2011 Feb 21. PMID:21339299<ref>PMID:21339299</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3qed" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Xylosidase 3D structures|Xylosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Cellvibrio japonicus Ueda107]] | |||
[[Category: Large Structures]] | |||
[[Category: Brumer H]] | |||
[[Category: Cartmell A]] | |||
[[Category: Gilbert HJ]] | |||
[[Category: Larsbrink J]] | |||
[[Category: Lewis RJ]] | |||
[[Category: Marles-Wright J]] | |||
[[Category: Mckee LS]] | |||
[[Category: Pena M]] | |||
[[Category: Viks-Nielsen A]] | |||
