View source for 5ysd


==Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose==
<StructureSection load='5ysd' size='340' side='right'caption='[[5ysd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ysd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_innocua_Clip11262 Listeria innocua Clip11262]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YSD 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]] 2.1&#8491;</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=5ysd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ysd OCA], [https://pdbe.org/5ysd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ysd RCSB], [https://www.ebi.ac.uk/pdbsum/5ysd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ysd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q92AS8_LISIN Q92AS8_LISIN] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
beta-1,2-Glucans are bacterial carbohydrates that exist in cyclic or linear forms and play an important role in infections and symbioses involving Gram-negative bacteria. Although several beta-1,2-glucan-associated enzymes have been characterized, little is known about how beta-1,2-glucan and its shorter oligosaccharides (Sopns) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of Sopn-binding protein (SO-BP, Lin1841) associated with the ABC transporter from the Gram-positive bacterium Listeria innocua Calorimetric analysis revealed that SO-BP specifically binds to Sopns with degree of polymerization of 3 or more, with Kd values in the micromolar range. The crystal structures of SO-BP in an unliganded open form and in closed complexes with tri-, tetra-, and pentaoligosaccharides (Sop3-5) were determined to a maximum resolution of 1.6 A. The binding site displayed shape complementarity to Sopn,which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop3-5by SO-BP, consistent with its binding thermodynamics. Computational free-energy calculations and a mutational analysis confirmed that interactions with the third glucose moiety of Sopns are significantly responsible for ligand binding. A reduction in unfavorable changes in binding entropy that were in proportion to the lengths of the Sopns were explained by conformational entropy changes. Phylogenetic and sequence analyses indicated that SO-BP ABC transporter homologs, glycoside hydrolases, and other related proteins are co-localized in the genomes of several bacteria. This study may improve our understanding of bacterial beta-1,2-glucan metabolism and promote discovery of unidentified beta-1,2-glucan-associated proteins.

Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua.,Abe K, Sunagawa N, Terada T, Takahashi Y, Arakawa T, Igarashi K, Samejima M, Nakai H, Taguchi H, Nakajima M, Fushinobu S J Biol Chem. 2018 Apr 20. pii: RA117.001536. doi: 10.1074/jbc.RA117.001536. PMID:29678880<ref>PMID:29678880</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ysd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Listeria innocua Clip11262]]
[[Category: Abe K]]
[[Category: Arakawa T]]
[[Category: Fushinobu S]]
[[Category: Nakajima M]]
[[Category: Taguchi H]]