5h40: Difference between revisions
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==Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with sophorose== | |||
<StructureSection load='5h40' size='340' side='right'caption='[[5h40]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5h40]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lachnoclostridium_phytofermentans_ISDg Lachnoclostridium phytofermentans ISDg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H40 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]] 2.2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5h40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h40 OCA], [https://pdbe.org/5h40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h40 RCSB], [https://www.ebi.ac.uk/pdbsum/5h40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h40 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A9KJS6_LACP7 A9KJS6_LACP7] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on beta-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-beta-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crystal structure. LpSOGP is a monomeric enzyme that contains a unique beta-sandwich domain (Ndom1) at its N-terminus. Unlike the dimeric GH94 enzymes possessing catalytic pockets at their dimer interface, LpSOGP has a catalytic pocket between Ndom1 and the catalytic domain. In the complex structure of LpSOGP with sophorose, sophorose binds at subsites +1 to +2. Notably, the Glc moiety at subsite +1 is flipped compared with the corresponding ligands in other GH94 enzymes. This inversion suggests the great distortion of the glycosidic bond between subsites -1 and +1, which is likely unfavorable for substrate binding. Compensation for this disadvantage at subsite +2 can be accounted for by the small distortion of the glycosidic bond in the sophorose molecule. Therefore, the binding mode at subsites +1 and +2 defines the substrate specificity of LpSOGP, which provides mechanistic insights into the substrate specificity of a phosphorylase acting on beta-1,2-glucooligosaccharides. | |||
Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans.,Nakajima M, Tanaka N, Furukawa N, Nihira T, Kodutsumi Y, Takahashi Y, Sugimoto N, Miyanaga A, Fushinobu S, Taguchi H, Nakai H Sci Rep. 2017 Feb 15;7:42671. doi: 10.1038/srep42671. PMID:28198470<ref>PMID:28198470</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5h40" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Lachnoclostridium phytofermentans ISDg]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Furukawa N]] | ||
[[Category: | [[Category: Fushinobu S]] | ||
[[Category: | [[Category: Kodutsumi Y]] | ||
[[Category: | [[Category: Miyanaga A]] | ||
[[Category: Nakai H]] | |||
[[Category: Nakajima M]] | |||
[[Category: Nihira T]] | |||
[[Category: Sugimoto N]] | |||
[[Category: Taguchi H]] | |||
[[Category: Takahashi Y]] | |||
[[Category: Tanaka N]] | |||
