3wl3 - Revision history

OCA at 08:45, 20 March 2024

OCA — Wed, 20 Mar 2024 08:45:49 GMT

←Older revision		Revision as of 08:45, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3wl3' size='340' side='right'caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3wl3' size='340' side='right'caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3wl4\|3wl4]], [[3we7\|3we7]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PH0499 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])~~</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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [https://pdbe.org/3wl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [https://www.ebi.ac.uk/pdbsum/3wl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wl3 ProSAT]</span></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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [https://pdbe.org/3wl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [https://www.ebi.ac.uk/pdbsum/3wl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wl3 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/O58235_PYRHO O58235_PYRHO]
-	In order to develop a structure-based understanding of the chitinolytic pathway in hyperthermophilic Pyrococcus species, we performed crystallographic studies on N,N'-diacetylchitobiose deacetylases (Dacs) from Pyrococcus horikoshii (Ph-Dac) and Pyrococcus furiosus (Pf-Dac). Neither Ph-Dac nor Pf-Dac was expressed in the soluble fraction of Escherichia coli harboring the expression plasmid. However, insertion of the target genes into the chromosome of E. coli yielded the soluble recombinant protein. The purified Pyrococcus Dacs were active and thermostable up to 85 degrees C. The crystal structures of Ph-Dac and Pf-Dac were determined at resolutions of 2.0 A and 1.54 A, respectively. The Pyrococcus Dac forms a hexamer composed of two trimers. These Dacs are characterized by an intermolecular cleft, which is formed by two polypeptides in the trimeric assembly. In Ph-Dac, catalytic Zn situated at the end of the cleft is coordinated by three side chain ligands from His44, Asp47, and His155, and by a phosphate ion derived from the crystallization reservoir solution. We considered that the bound phosphate mimicked the tetrahedral oxyanion, which is an intermediate of hydrolysis of the N-acetyl group, and proposed an appropriate reaction mechanism. In the proposed mechanism, the Nepsilon atom of His264 (from the adjacent polypeptide in the Ph-Dac sequence) is directly involved in the stabilization of the oxyanion intermediate. Mutation analysis also indicated that His264 was essential to the catalysis. These factors give the archaeal Dacs an unprecedented active site architecture a Zn-dependent deacetylases. DATABASE: Structural data are available in the Protein Data Bank database under accession numbers 3WL3, 3WL4, and 3WE7. STRUCTURED DIGITAL ABSTRACT: Ph-Dac and Ph-Dac bind by x-ray crystallography (View interaction) Pf-Dac and Pf-Dac bind by x-ray crystallography (View interaction).	+
-		+
-	Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase.,Mine S, Niiyama M, Hashimoto W, Ikegami T, Koma D, Ohmoto T, Fukuda Y, Inoue T, Abe Y, Ueda T, Morita J, Uegaki K, Nakamura T FEBS J. 2014 Apr 7. doi: 10.1111/~~febs.12805. PMID:24702737<ref>PMID:24702737<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3wl3" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pyrococcus horikoshii]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	[[Category: Hashimoto, W]]	+	[[Category: Hashimoto W]]
-	[[Category: Nakamura, T]]	+	[[Category: Nakamura T]]
-	[[Category: Niiyama, M]]	+	[[Category: Niiyama M]]
-	[[Category: Uegaki, K]]	+	[[Category: Uegaki K]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Zn-dependent deacetylase~~]]	+

OCA at 05:40, 3 August 2022

OCA — Wed, 03 Aug 2022 05:40:49 GMT

←Older revision		Revision as of 05:40, 3 August 2022
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	==N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii==		==N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii==
-	<StructureSection load='3wl3' size='340' side='right' caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3wl3' size='340' side='right'caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wl4\|3wl4]], [[3we7\|3we7]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0499 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0499 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [~~http~~://pdbe.org/3wl3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wl3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wl3 ProSAT]</span></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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [https://pdbe.org/3wl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [https://www.ebi.ac.uk/pdbsum/3wl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wl3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]

OCA at 08:59, 21 February 2019

OCA — Thu, 21 Feb 2019 08:59:50 GMT

←Older revision		Revision as of 08:59, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='3wl3' size='340' side='right' caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3wl3' size='340' side='right' caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0499 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://pdbe.org/3wl3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wl3 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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://pdbe.org/3wl3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wl3 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pyrococcus horikoshii]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]
	[[Category: Nakamura, T]]		[[Category: Nakamura, T]]

OCA at 13:18, 11 August 2016

OCA — Thu, 11 Aug 2016 13:18:27 GMT

←Older revision		Revision as of 13:18, 11 August 2016
Line 1:		Line 1:
		+
	==N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii==		==N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii==
	<StructureSection load='3wl3' size='340' side='right' caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3wl3' size='340' side='right' caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://pdbe.org/3wl3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wl3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3wl3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:11, 5 January 2015

OCA — Mon, 05 Jan 2015 14:11:41 GMT

←Older revision		Revision as of 14:11, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<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: Hashimoto, W.]]	+	[[Category: Hashimoto, W]]
-	[[Category: Nakamura, T.]]	+	[[Category: Nakamura, T]]
-	[[Category: Niiyama, M.]]	+	[[Category: Niiyama, M]]
-	[[Category: Uegaki, K.]]	+	[[Category: Uegaki, K]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Zn-dependent deacetylase]]		[[Category: Zn-dependent deacetylase]]

OCA at 13:26, 20 August 2014

OCA — Wed, 20 Aug 2014 13:26:27 GMT

←Older revision		Revision as of 13:26, 20 August 2014
Line 2:		Line 2:
	<StructureSection load='3wl3' size='340' side='right' caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3wl3' size='340' side='right' caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. <br>	+	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>		</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</td></tr>		<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 PDBsum]</span></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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 PDBsum]</span></td></tr>
	<table>		<table>
Line 14:		Line 13:
	Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase.,Mine S, Niiyama M, Hashimoto W, Ikegami T, Koma D, Ohmoto T, Fukuda Y, Inoue T, Abe Y, Ueda T, Morita J, Uegaki K, Nakamura T FEBS J. 2014 Apr 7. doi: 10.1111/febs.12805. PMID:24702737<ref>PMID:24702737</ref>		Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase.,Mine S, Niiyama M, Hashimoto W, Ikegami T, Koma D, Ohmoto T, Fukuda Y, Inoue T, Abe Y, Ueda T, Morita J, Uegaki K, Nakamura T FEBS J. 2014 Apr 7. doi: 10.1111/febs.12805. PMID:24702737<ref>PMID:24702737</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==

OCA at 08:13, 7 May 2014

OCA — Wed, 07 May 2014 08:13:51 GMT

←Older revision		Revision as of 08:13, 7 May 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii==
		+	<StructureSection load='3wl3' size='340' side='right' caption='[[3wl3]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wl4\|3wl4]], [[3we7\|3we7]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In order to develop a structure-based understanding of the chitinolytic pathway in hyperthermophilic Pyrococcus species, we performed crystallographic studies on N,N'-diacetylchitobiose deacetylases (Dacs) from Pyrococcus horikoshii (Ph-Dac) and Pyrococcus furiosus (Pf-Dac). Neither Ph-Dac nor Pf-Dac was expressed in the soluble fraction of Escherichia coli harboring the expression plasmid. However, insertion of the target genes into the chromosome of E. coli yielded the soluble recombinant protein. The purified Pyrococcus Dacs were active and thermostable up to 85 degrees C. The crystal structures of Ph-Dac and Pf-Dac were determined at resolutions of 2.0 A and 1.54 A, respectively. The Pyrococcus Dac forms a hexamer composed of two trimers. These Dacs are characterized by an intermolecular cleft, which is formed by two polypeptides in the trimeric assembly. In Ph-Dac, catalytic Zn situated at the end of the cleft is coordinated by three side chain ligands from His44, Asp47, and His155, and by a phosphate ion derived from the crystallization reservoir solution. We considered that the bound phosphate mimicked the tetrahedral oxyanion, which is an intermediate of hydrolysis of the N-acetyl group, and proposed an appropriate reaction mechanism. In the proposed mechanism, the Nepsilon atom of His264 (from the adjacent polypeptide in the Ph-Dac sequence) is directly involved in the stabilization of the oxyanion intermediate. Mutation analysis also indicated that His264 was essential to the catalysis. These factors give the archaeal Dacs an unprecedented active site architecture a Zn-dependent deacetylases. DATABASE: Structural data are available in the Protein Data Bank database under accession numbers 3WL3, 3WL4, and 3WE7. STRUCTURED DIGITAL ABSTRACT: Ph-Dac and Ph-Dac bind by x-ray crystallography (View interaction) Pf-Dac and Pf-Dac bind by x-ray crystallography (View interaction).

-	~~The entry 3wl3 is ON HOLD until Paper Publication~~	+	Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase.,Mine S, Niiyama M, Hashimoto W, Ikegami T, Koma D, Ohmoto T, Fukuda Y, Inoue T, Abe Y, Ueda T, Morita J, Uegaki K, Nakamura T FEBS J. 2014 Apr 7. doi: 10.1111/febs.12805. PMID:24702737<ref>PMID:24702737</ref>

-	~~Authors~~: Nakamura, T., Niiyama, M.~~, Hashimoto, W.,~~ Uegaki, K.	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~N,N'~~-~~diacetylchitobiose~~ deacetylase ~~from Pyrococcus horikoshii~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hashimoto, W.]]
		+	[[Category: Nakamura, T.]]
		+	[[Category: Niiyama, M.]]
		+	[[Category: Uegaki, K.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Zn-dependent deacetylase]]

OCA at 12:32, 20 November 2013

OCA — Wed, 20 Nov 2013 12:32:55 GMT

←Older revision		Revision as of 12:32, 20 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3wl3 is ON HOLD	+	The entry 3wl3 is ON HOLD until Paper Publication

	Authors: Nakamura, T., Niiyama, M., Hashimoto, W., Uegaki, K.		Authors: Nakamura, T., Niiyama, M., Hashimoto, W., Uegaki, K.

	Description: N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii		Description: N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii

OCA: Protected "3wl3" [edit=sysop:move=sysop]

OCA — Wed, 13 Nov 2013 07:07:25 GMT

Protected "3wl3" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:07, 13 November 2013

OCA: New page: '''Unreleased structure''' The entry 3wl3 is ON HOLD Authors: Nakamura, T., Niiyama, M., Hashimoto, W., Uegaki, K. Description: N,N'-diacetylchitobiose deacetylase from Pyrococcus hori...

OCA — Wed, 13 Nov 2013 07:07:24 GMT

New page: '''Unreleased structure''' The entry 3wl3 is ON HOLD Authors: Nakamura, T., Niiyama, M., Hashimoto, W., Uegaki, K. Description: N,N'-diacetylchitobiose deacetylase from Pyrococcus hori...

New page

'''Unreleased structure'''

The entry 3wl3 is ON HOLD

Authors: Nakamura, T., Niiyama, M., Hashimoto, W., Uegaki, K.

Description: N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii