4yzp - Revision history

OCA at 08:10, 27 September 2023

OCA — Wed, 27 Sep 2023 08:10:19 GMT

←Older revision		Revision as of 08:10, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yzp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YZP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yzp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YZP 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=4yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yzp OCA], [https://pdbe.org/4yzp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yzp RCSB], [https://www.ebi.ac.uk/pdbsum/4yzp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yzp 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]] 1.7Å</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=4yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yzp OCA], [https://pdbe.org/4yzp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yzp RCSB], [https://www.ebi.ac.uk/pdbsum/4yzp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yzp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:33, 10 May 2023

OCA — Wed, 10 May 2023 07:33:08 GMT

←Older revision		Revision as of 07:33, 10 May 2023
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	<StructureSection load='4yzp' size='340' side='right'caption='[[4yzp]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4yzp' size='340' side='right'caption='[[4yzp]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yzp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"clostridium_licheniforme"_weigmann_1898 "clostridium licheniforme" weigmann 1898~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YZP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YZP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yzp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YZP FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cel5C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1402 "Clostridium licheniforme" Weigmann 1898])</td></tr>	+	</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=4yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yzp OCA], [https://pdbe.org/4yzp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yzp RCSB], [https://www.ebi.ac.uk/pdbsum/4yzp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yzp ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulase Cellulase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] </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=4yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yzp OCA], [~~http~~://pdbe.org/4yzp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yzp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yzp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yzp ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q65JI7_BACLD Q65JI7_BACLD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Clostridium licheniforme weigmann 1898]]~~	+	[[Category: Bacillus licheniformis]]
-	~~[[Category: Cellulase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liberato~~, M V~~]]	+	[[Category: Liberato MV]]
-	[[Category: Polikarpov, I]]	+	[[Category: Polikarpov I]]
-	[[Category: Popov, A]]	+	[[Category: Popov A]]
-	~~[[Category: Endoglucanase]]~~	+
-	~~[[Category: Gh5]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Tri-modular~~]]	+

OCA at 08:47, 1 January 2020

OCA — Wed, 01 Jan 2020 08:47:22 GMT

←Older revision		Revision as of 08:47, 1 January 2020
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	==See Also==		==See Also==
-	*[[Glucanase\|Glucanase]]	+	*[[Glucanase 3D structures\|Glucanase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:18, 17 April 2019

OCA — Wed, 17 Apr 2019 06:18:46 GMT

←Older revision		Revision as of 06:18, 17 April 2019
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	==Crystal structure of a tri-modular GH5 (subfamily 4) endo-beta-1, 4-glucanase from Bacillus licheniformis==		==Crystal structure of a tri-modular GH5 (subfamily 4) endo-beta-1, 4-glucanase from Bacillus licheniformis==
-	<StructureSection load='4yzp' size='340' side='right' caption='[[4yzp]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4yzp' size='340' side='right'caption='[[4yzp]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yzp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"clostridium_licheniforme"_weigmann_1898 "clostridium licheniforme" weigmann 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YZP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yzp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"clostridium_licheniforme"_weigmann_1898 "clostridium licheniforme" weigmann 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YZP FirstGlance]. <br>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 4yzp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4yzp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glucanase\|Glucanase]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 26:
	[[Category: Clostridium licheniforme weigmann 1898]]		[[Category: Clostridium licheniforme weigmann 1898]]
	[[Category: Cellulase]]		[[Category: Cellulase]]
		+	[[Category: Large Structures]]
	[[Category: Liberato, M V]]		[[Category: Liberato, M V]]
	[[Category: Polikarpov, I]]		[[Category: Polikarpov, I]]

OCA at 09:42, 22 November 2017

OCA — Wed, 22 Nov 2017 09:42:30 GMT

←Older revision		Revision as of 09:42, 22 November 2017
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	<StructureSection load='4yzp' size='340' side='right' caption='[[4yzp]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4yzp' size='340' side='right' caption='[[4yzp]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yzp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YZP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yzp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"clostridium_licheniforme"_weigmann_1898 "clostridium licheniforme" weigmann 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YZP FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulase Cellulase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cel5C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1402 "Clostridium licheniforme" Weigmann 1898])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulase Cellulase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] </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=4yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yzp OCA], [http://pdbe.org/4yzp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yzp RCSB], [http://www.ebi.ac.uk/pdbsum/4yzp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yzp ProSAT]</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=4yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yzp OCA], [http://pdbe.org/4yzp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yzp RCSB], [http://www.ebi.ac.uk/pdbsum/4yzp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yzp ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clostridium licheniforme weigmann 1898]]
	[[Category: Cellulase]]		[[Category: Cellulase]]
	[[Category: Liberato, M V]]		[[Category: Liberato, M V]]

OCA at 10:55, 2 November 2016

OCA — Wed, 02 Nov 2016 10:55:41 GMT

←Older revision		Revision as of 10:55, 2 November 2016
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	<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=4yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yzp OCA], [http://pdbe.org/4yzp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yzp RCSB], [http://www.ebi.ac.uk/pdbsum/4yzp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yzp ProSAT]</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=4yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yzp OCA], [http://pdbe.org/4yzp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yzp RCSB], [http://www.ebi.ac.uk/pdbsum/4yzp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yzp ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.
		+
		+	Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism.,Liberato MV, Silveira RL, Prates ET, de Araujo EA, Pellegrini VO, Camilo CM, Kadowaki MA, Neto Mde O, Popov A, Skaf MS, Polikarpov I Sci Rep. 2016 Apr 1;6:23473. doi: 10.1038/srep23473. PMID:27032335<ref>PMID:27032335</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4yzp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:00, 10 September 2016

OCA — Sat, 10 Sep 2016 21:00:09 GMT

←Older revision		Revision as of 21:00, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 4yzp is ON HOLD until Paper Publication~~	+	==Crystal structure of a tri-modular GH5 (subfamily 4) endo-beta-1, 4-glucanase from Bacillus licheniformis==
-		+	<StructureSection load='4yzp' size='340' side='right' caption='[[4yzp]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors: Liberato, M.V., Popov, A., Polikarpov, I.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4yzp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YZP FirstGlance]. <br>
-	~~Description:~~ Crystal structure of a tri-modular GH5 (subfamily 4) endo-beta-1, 4-glucanase from Bacillus licheniformis	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulase Cellulase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] </span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=4yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yzp OCA], [http://pdbe.org/4yzp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yzp RCSB], [http://www.ebi.ac.uk/pdbsum/4yzp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yzp ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cellulase]]
		+	[[Category: Liberato, M V]]
		+	[[Category: Polikarpov, I]]
	[[Category: Popov, A]]		[[Category: Popov, A]]
-	[[Category: ~~Liberato, M.V~~]]	+	[[Category: Endoglucanase]]
-	[[Category: ~~Polikarpov, I~~]]	+	[[Category: Gh5]]
		+	[[Category: Hydrolase]]
		+	[[Category: Tri-modular]]

OCA at 23:47, 30 November 2015

OCA — Mon, 30 Nov 2015 23:47:58 GMT

←Older revision		Revision as of 23:47, 30 November 2015
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Popov, A]]		[[Category: Popov, A]]
-	[[Category: Polikarpov, I]]
	[[Category: Liberato, M.V]]		[[Category: Liberato, M.V]]
		+	[[Category: Polikarpov, I]]

OCA at 11:19, 22 April 2015

OCA — Wed, 22 Apr 2015 11:19:39 GMT

←Older revision		Revision as of 11:19, 22 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4yzp is ON HOLD	+	The entry 4yzp is ON HOLD until Paper Publication

	Authors: Liberato, M.V., Popov, A., Polikarpov, I.		Authors: Liberato, M.V., Popov, A., Polikarpov, I.

OCA: Protected "4yzp" [edit=sysop:move=sysop]

OCA — Wed, 01 Apr 2015 12:06:45 GMT

Protected "4yzp" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:06, 1 April 2015