2zyk - Revision history

OCA at 13:58, 13 March 2024

2024-03-13T13:58:58Z

← Older revision		Revision as of 13:58, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2zyk' size='340' side='right'caption='[[2zyk]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2zyk' size='340' side='right'caption='[[2zyk]], [[Resolution\|resolution]] 2.50Å' 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]] 2.5Å</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]]
Line 17:		Line 20:
	</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®/PubMed®, 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~~]]

OCA at 12:11, 29 July 2020

2020-07-29T12:11:45Z

← Older revision		Revision as of 12:11, 29 July 2020
Line 1:		Line 1:

	==Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin==		==Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin==
	<StructureSection load='2zyk' size='340' side='right' caption='[[2zyk]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2zyk' size='340' side='right'caption='[[2zyk]], [[Resolution\|resolution]] 2.50Å' 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://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZYK FirstGlance]. <br>		<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>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>		</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>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca.weizmann.ac~~.~~il/oca-docs~~/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='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>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43649]]		[[Category: Atcc 43649]]
			[[Category: Large Structures]]
	[[Category: Ichikawa, K]]		[[Category: Ichikawa, K]]
	[[Category: Kamitori, S]]		[[Category: Kamitori, S]]

OCA at 07:02, 18 October 2018

2018-10-18T07:02:01Z

← Older revision		Revision as of 07:02, 18 October 2018
Line 11:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zy/2zyk_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zy/2zyk_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 18:52, 11 August 2016

2016-08-11T18:52:28Z

← Older revision		Revision as of 18:52, 11 August 2016
Line 1:		Line 1:

	==Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin==		==Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin==
	<StructureSection load='2zyk' size='340' side='right' caption='[[2zyk]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2zyk' size='340' side='right' caption='[[2zyk]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zyk]] is a 4 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZYK FirstGlance]. <br>		<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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZYK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zyk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zyk RCSB], [http://www.ebi.ac.uk/pdbsum/2zyk PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/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>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ 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;">		<div style="background-color:#fffaf0;">
Line 24:		Line 25:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2zyk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Thermoactinomyces vulgaris~~]]		[[Category: Atcc 43649]]
	[[Category: Ichikawa, K]]		[[Category: Ichikawa, K]]
	[[Category: Kamitori, S]]		[[Category: Kamitori, S]]

OCA at 09:06, 20 January 2015

2015-01-20T09:06:19Z

← Older revision		Revision as of 09:06, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zyk]] is a 4 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZYK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zyk]] is a 4 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZYK FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zyk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zyk RCSB], [http://www.ebi.ac.uk/pdbsum/2zyk PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zyk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zyk RCSB], [http://www.ebi.ac.uk/pdbsum/2zyk PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Thermoactinomyces vulgaris]]		[[Category: Thermoactinomyces vulgaris]]
	[[Category: Ichikawa, K.]]		[[Category: Ichikawa, K]]
	[[Category: Kamitori, S.]]		[[Category: Kamitori, S]]
	[[Category: Matsumoto, N.]]		[[Category: Matsumoto, N]]
	[[Category: Mizuno, M.]]		[[Category: Mizuno, M]]
	[[Category: Nishikawa, A.]]		[[Category: Nishikawa, A]]
	[[Category: Sakano, Y.]]		[[Category: Sakano, Y]]
	[[Category: Sogawa, A.]]		[[Category: Sogawa, A]]
	[[Category: Tonozuka, T.]]		[[Category: Tonozuka, T]]
	[[Category: Yamada, M.]]		[[Category: Yamada, M]]
	[[Category: Yoshida, H.]]		[[Category: Yoshida, H]]
	[[Category: Closed form]]		[[Category: Closed form]]
	[[Category: Solute-binding protein]]		[[Category: Solute-binding protein]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA at 05:23, 2 October 2014

2014-10-02T05:23:01Z

← Older revision		Revision as of 05:23, 2 October 2014
Line 1:		Line 1:
	[[Image:~~2zyk~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin==
			<StructureSection load='2zyk' size='340' side='right' caption='[[2zyk]], [[Resolution\|resolution]] 2.50Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2zyk]] is a 4 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZYK FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene><br>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zyk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zyk RCSB], [http://www.ebi.ac.uk/pdbsum/2zyk PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zy/2zyk_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</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/chain_selection.php?pdb_ID=2ata ConSurf].
			<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.

	~~{{STRUCTURE_2zyk\| PDB=2zyk \| SCENE= }}~~		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>

	~~===Crystal structure of cyclo~~/~~maltodextrin-binding protein complexed with gamma-cyclodextrin===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17371546}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2zyk]] is~~ a ~~4 chain structure with sequence from [http://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].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017371546<~~/~~ref~~><~~ref group="xtra">PMID:019490104</ref><references group="xtra"~~/>
	[[Category: Thermoactinomyces vulgaris]]		[[Category: Thermoactinomyces vulgaris]]
	[[Category: Ichikawa, K.]]		[[Category: Ichikawa, K.]]

OCA: Protected "2zyk" [edit=sysop:move=sysop]

2013-01-07T21:22:07Z

Protected "2zyk" [edit=sysop:move=sysop]

← Older revision	Revision as of 21:22, 7 January 2013
(No difference)

OCA at 21:22, 7 January 2013

2013-01-07T21:22:05Z

← Older revision		Revision as of 21:22, 7 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2zyk.png\|left\|200px]]		[[Image:2zyk.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2zyk", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2zyk\| PDB=2zyk \| SCENE= }}		{{STRUCTURE_2zyk\| PDB=2zyk \| SCENE= }}

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


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17371546}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17371546 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17371546}}		{{ABSTRACT_PUBMED_17371546}}

	==About this Structure==		==About this Structure==
	~~2ZYK~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://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].		[[2zyk]] is a 4 chain structure with sequence from [http://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].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17371546~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017371546</ref><ref group="xtra">PMID:019490104</ref><references group="xtra"/>
	[[Category: Thermoactinomyces vulgaris]]		[[Category: Thermoactinomyces vulgaris]]
	[[Category: Ichikawa, K.]]		[[Category: Ichikawa, K.]]
Line 38:		Line 26:
	[[Category: Solute-binding protein]]		[[Category: Solute-binding protein]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 3 09:37:20 2009''~~

OCA at 06:37, 3 June 2009

2009-06-03T06:37:21Z

← Older revision		Revision as of 06:37, 3 June 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
	[[Image:2zyk.~~jpg~~\|left\|200px]]		[[Image:2zyk.png\|left\|200px]]

	<!--		<!--
Line 39:		Line 39:
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 11 12~~:39:16 2009''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 3 09:37:20 2009''

OCA at 10:39, 11 February 2009

2009-02-11T10:39:16Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+{{Seed}}
-The entry 2zyk is ON HOLD
+<!--
-Authors: Tonozuka, T., Sogawa, A., Yamada, M., Matsumoto, N., Yoshida, H., Kamitori, S., Ichikawa, K., Mizuno, M., Nishikawa, A., Sakano, Y.
+===Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin===
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 11 12:34:33 2009''
+<!--