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7ebi
From Proteopedia
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==Chitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitotetraose.== | ==Chitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitotetraose.== | ||
| - | <StructureSection load='7ebi' size='340' side='right'caption='[[7ebi]]' scene=''> | + | <StructureSection load='7ebi' size='340' side='right'caption='[[7ebi]], [[Resolution|resolution]] 1.50Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6lzr 6lzr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7ebi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_harveyi_1DA3 Vibrio harveyi 1DA3]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6lzr 6lzr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBI FirstGlance]. <br> |
| - | </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=7ebi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebi OCA], [https://pdbe.org/7ebi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebi RCSB], [https://www.ebi.ac.uk/pdbsum/7ebi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebi ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=7ebi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebi OCA], [https://pdbe.org/7ebi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebi RCSB], [https://www.ebi.ac.uk/pdbsum/7ebi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebi ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/D0XC84_VIBH1 D0XC84_VIBH1] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | VhCBP is a periplasmic chitooligo saccharide-specific binding protein mainly responsible for translocation of the chitooligosaccharide (GlcNAc)2 across the double membranes of marine bacteria Vibrio harveyi. However, structural and thermodynamic understanding of the sugar binding/release processes of VhCBP are relatively unknown. VhCBP displayed the greatest affinity towards (GlcNAc)2, with lower affinity for longer-chain chitooligosaccharides [(GlcNAc)3-4]. (GlcNAc)4 partially occupied the closed sugar-binding groove, with two reducing-end GlcNAc units extending beyond the sugar-binding groove and barely characterized by weak electron density. Mutation of three conserved residues (Trp(363), Asp(365) and Trp(513)) to Ala resulted in drastic decreases in the binding affinity towards the preferred substrate (GlcNAc)2, indicating their significant contributions to sugar binding. The structure of the W513A-(GlcNAc)2 complex in a 'half-open' conformation unveiled the intermediary step of the (GlcNAc)2 translocation from the soluble CBP in periplasm to the inner membrane-transporting components. Isothermal calorimetry data suggested that VhCBP adopts the high affinity conformation to bind (GlcNAc)2, whilst its low affinity conformation facilitated sugar release. Thus, chitooligosaccharide translocation, conferred by periplasmic VhCBP, is a crucial step in the chitin catabolic pathway, allowing Vibrio bacteria to thrive in oceans where chitin is their major source of nutrients. | ||
| + | |||
| + | A structural model for (GlcNAc)2 translocation via a periplasmic chitooligosaccharide binding protein from marine Vibrio bacteria.,Kitaoku Y, Fukamizo T, Kumsaoad S, Ubonbal P, Robinson RC, Suginta W J Biol Chem. 2021 Aug 13:101071. doi: 10.1016/j.jbc.2021.101071. PMID:34400168<ref>PMID:34400168</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7ebi" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Vibrio harveyi 1DA3]] | ||
[[Category: Kitaoku Y]] | [[Category: Kitaoku Y]] | ||
[[Category: Robinson RC]] | [[Category: Robinson RC]] | ||
Current revision
Chitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitotetraose.
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