2zyk: Difference between revisions

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<StructureSection load='2zyk' size='340' side='right'caption='[[2zyk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='2zyk' size='340' side='right'caption='[[2zyk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2zyk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43649 Atcc 43649]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dfz 2dfz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZYK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2ZYK FirstGlance]. <br>
<table><tr><td colspan='2'>[[2zyk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dfz 2dfz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZYK FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></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]] 2.5&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2zyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zyk OCA], [http://pdbe.org/2zyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zyk RCSB], [http://www.ebi.ac.uk/pdbsum/2zyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zyk ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900042:gamma-cyclodextrin'>PRD_900042</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=2zyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zyk OCA], [https://pdbe.org/2zyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zyk RCSB], [https://www.ebi.ac.uk/pdbsum/2zyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zyk ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9AJF5_THEVU Q9AJF5_THEVU]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zyk ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zyk ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of a Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein (TvuCMBP) complexed with gamma-cyclodextrin has been determined. Like Escherichia coli maltodextrin-binding protein (EcoMBP) and other bacterial sugar-binding proteins, TvuCMBP consists of two domains, an N- and a C-domain, both of which are composed of a central beta-sheet surrounded by alpha-helices; the domains are joined by a hinge region containing three segments. gamma-Cyclodextrin is located at a cleft formed by the two domains. A common functional conformational change has been reported in this protein family, which involves switching from an open form to a sugar-transporter bindable form, designated a closed form. The TvuCMBP-gamma-cyclodextrin complex structurally resembles the closed form of EcoMBP, indicating that TvuCMBP complexed with gamma-cyclodextrin adopts the closed form. The fluorescence measurements also showed that the affinities of TvuCMBP for cyclodextrins were almost equal to those for maltooligosaccharides. Despite having similar folds, the sugar-binding site of the N-domain part of TvuCMBP and other bacterial sugar-binding proteins are strikingly different. In TvuCMBP, the side-chain of Leu59 protrudes from the N-domain part into the sugar-binding cleft and orients toward the central cavity of gamma-cyclodextrin, thus Leu59 appears to play the key role in binding. The cleft of the sugar-binding site of TvuCMBP is also wider than that of EcoMBP. These findings suggest that the sugar-binding site of the N-domain part and the wide cleft are critical in determining the specificity of TvuCMBP for gamma-cyclodextrin.
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.,Tonozuka T, Sogawa A, Yamada M, Matsumoto N, Yoshida H, Kamitori S, Ichikawa K, Mizuno M, Nishikawa A, Sakano Y FEBS J. 2007 Apr;274(8):2109-20. Epub 2007 Mar 20. PMID:17371546<ref>PMID:17371546</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2zyk" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 43649]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ichikawa, K]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Kamitori, S]]
[[Category: Ichikawa K]]
[[Category: Matsumoto, N]]
[[Category: Kamitori S]]
[[Category: Mizuno, M]]
[[Category: Matsumoto N]]
[[Category: Nishikawa, A]]
[[Category: Mizuno M]]
[[Category: Sakano, Y]]
[[Category: Nishikawa A]]
[[Category: Sogawa, A]]
[[Category: Sakano Y]]
[[Category: Tonozuka, T]]
[[Category: Sogawa A]]
[[Category: Yamada, M]]
[[Category: Tonozuka T]]
[[Category: Yoshida, H]]
[[Category: Yamada M]]
[[Category: Closed form]]
[[Category: Yoshida H]]
[[Category: Solute-binding protein]]
[[Category: Sugar binding protein]]

Latest revision as of 13:58, 13 March 2024

Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin

2zyk, resolution 2.50Å

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