4ak6: Difference between revisions

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-[[Image:4ak6.jpg|left|200px]]
-<!--
+==BpGH117_H302E mutant glycoside hydrolase==
-The line below this paragraph, containing "STRUCTURE_4ak6", creates the "Structure Box" on the page.
+<StructureSection load='4ak6' size='340' side='right'caption='[[4ak6]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[4ak6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phocaeicola_plebeius Phocaeicola plebeius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AK6 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_4ak6|  PDB=4ak6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ak6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ak6 OCA], [https://pdbe.org/4ak6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ak6 RCSB], [https://www.ebi.ac.uk/pdbsum/4ak6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ak6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/B5CY74_PHOPM B5CY74_PHOPM]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Agars are abundant polysaccharides from marine red algae and their chemical structure consists of alternating D- galactose and 3,6-anhydro-L-galactose residues, the latter of which is presumed to make the polymer recalcitrant to degradation by most terrestrial bacteria. Here we study a family 117 glycoside hydrolase (BpGH117) encoded within a recently discovered locus from the human gut bacterium Bacteroides plebeius. Consistent with this locus being involved in agarocolloid degradation, we show BpGH117 is an exo-acting 3,6-anhydro-alpha-(1,3)-L-galactosidase that removes the 3,6-anhydro-galactose from the non-reducing end of neoagaro-oligosaccharides. A Michaelis-complex of BpGH117 with neoagarobiose reveals the distortion of the constrained 3,6-anhydro-L-galactose into a conformation that favours catalysis. Furthermore, this complex, supported by analysis of site-directed mutants, provides evidence for and organization of the active site and positioning of the catalytic residues that is consistent with an inverting mechanism of catalysis and suggests that a histidine residue acts as the general acid. This latter feature differs from the vast majority of glycoside hydrolases, which use a carboxylic acid, highlighting the alternative strategies that enzymes may employ in catalyzing the cleavage of glycosidic bonds.
-===BpGH117_H302E mutant glycoside hydrolase===
+Analysis of a keystone enzyme in agar hydrolysis provides insight into polysaccharide degradation from red seaweeds.,Hehemann JH, Smyth L, Yadav A, Vocadlo DJ, Boraston AB J Biol Chem. 2012 Mar 5. PMID:22393053<ref>PMID:22393053</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4ak6" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22393053}}, adds the Publication Abstract to the page
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22393053 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22393053}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[4ak6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_plebeius Bacteroides plebeius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AK6 OCA].
+[[Category: Phocaeicola plebeius]]
+[[Category: Boraston AB]]
-==Reference==
+[[Category: Hehemann JH]]
-<ref group="xtra">PMID:022393053</ref><references group="xtra"/>
+[[Category: Smyth L]]
-[[Category: Bacteroides plebeius]]
+[[Category: Vocadlo DJ]]
-[[Category: Boraston, A B.]]
+[[Category: Yadav A]]
-[[Category: Hehemann, J H.]]
-[[Category: Smyth, L.]]
-[[Category: Vocadlo, D J.]]
-[[Category: Yadav, A.]]
-[[Category: Hydrolase]]