1k5c - Revision history

OCA at 07:57, 3 April 2024

OCA — Wed, 03 Apr 2024 07:57:57 GMT

←Older revision		Revision as of 07:57, 3 April 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K5C FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K5C FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 0.96Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1kcc\|1kcc]], [[1kcd\|1kcd]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15]~~ </~~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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [https://pdbe.org/1k5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [https://www.ebi.ac.uk/pdbsum/1k5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5c 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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [https://pdbe.org/1k5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [https://www.ebi.ac.uk/pdbsum/1k5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5c ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/P79074_9AGAR P79074_9AGAR]
	== 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=1k5c 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=1k5c ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Crystal structures of endopolygalacturonase from Stereum purpureum were solved in native and two galacturonic acid complex states at atomic resolution. Endopolygalacturonase catalyzes the hydrolysis of alpha-1,4-glycosidic linkage of polygalacturonate in pectin. The native structure was determined by the multiple wavelength anomalous dispersion method and was refined anisotropically with SHELXL-97, with an R factor of 11.4% and an R(free) factor of 14.0% at 0.96 A resolution. The enzyme folds into a right-handed parallel beta-helix with 10 complete turns. The crystal structures of its binary complex with one D-galacturonate and its ternary complex with two D-galacturonates were also determined to identify the substrate binding site at 1.0 and 1.15 A resolutions, respectively. In the binary complex, one beta-D-galactopyranuronate was found in the +1 subsite, thus proving the strong affinity of the +1 subsite expected from the bond cleavage frequency on oligogalacturonates. In the ternary complex, an additional beta-D-galactofuranuronate was found in the -1 subsite. In both subsites, the recognition of the galacturonate carboxy group is important in galacturonate binding. In the +1 subsite, the carboxy group interacts with three basic residues, His195, Arg226, and Lys228, which were conserved in all endopolygalacturonases. In the -1 subsite, the unique nonprolyl cis-peptide bond is believed to be involved in binding the carboxy group of the substrate. The active site architecture of the complexes provides insight into the mechanism of inverting glycosyl hydrolases and also sheds light on the basis of the differences between the family 28 and the other inverting glycosyl hydrolases.
-
-	Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.,Shimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H Biochemistry. 2002 May 28;41(21):6651-9. PMID:12022868<ref>PMID:12022868</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1k5c" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Chondrostereum purpureum]]		[[Category: Chondrostereum purpureum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Polygalacturonase]]~~	+	[[Category: Kato H]]
-	[[Category: Kato, H]]	+	[[Category: Miyairi K]]
-	[[Category: Miyairi, K]]	+	[[Category: Nakatsu T]]
-	[[Category: Nakatsu, T]]	+	[[Category: Okuno T]]
-	[[Category: Okuno, T]]	+	[[Category: Shimizu T]]
-	[[Category: Shimizu, T]]	+
-	~~[[Category: Beta helical structure]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Silver-leaf inducing substance~~]]	+

OCA at 06:49, 11 August 2021

OCA — Wed, 11 Aug 2021 06:49:36 GMT

←Older revision		Revision as of 06:49, 11 August 2021
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	<StructureSection load='1k5c' size='340' side='right'caption='[[1k5c]], [[Resolution\|resolution]] 0.96Å' scene=''>		<StructureSection load='1k5c' size='340' side='right'caption='[[1k5c]], [[Resolution\|resolution]] 0.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1K5C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K5C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kcc\|1kcc]], [[1kcd\|1kcd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kcc\|1kcc]], [[1kcd\|1kcd]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [~~http~~://pdbe.org/1k5c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1k5c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5c 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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [https://pdbe.org/1k5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [https://www.ebi.ac.uk/pdbsum/1k5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5c ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 09:16, 6 November 2019

OCA — Wed, 06 Nov 2019 09:16:44 GMT

←Older revision		Revision as of 09:16, 6 November 2019
Line 1:		Line 1:

	==Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution==		==Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution==
-	<StructureSection load='1k5c' size='340' side='right' caption='[[1k5c]], [[Resolution\|resolution]] 0.96Å' scene=''>	+	<StructureSection load='1k5c' size='340' side='right'caption='[[1k5c]], [[Resolution\|resolution]] 0.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K5C FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K5C FirstGlance]. <br>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Chondrostereum purpureum]]		[[Category: Chondrostereum purpureum]]
		+	[[Category: Large Structures]]
	[[Category: Polygalacturonase]]		[[Category: Polygalacturonase]]
	[[Category: Kato, H]]		[[Category: Kato, H]]

OCA at 21:26, 24 January 2018

OCA — Wed, 24 Jan 2018 21:26:36 GMT

←Older revision		Revision as of 21:26, 24 January 2018
Line 1:		Line 1:
		+
	==Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution==		==Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution==
	<StructureSection load='1k5c' size='340' side='right' caption='[[1k5c]], [[Resolution\|resolution]] 0.96Å' scene=''>		<StructureSection load='1k5c' size='340' side='right' caption='[[1k5c]], [[Resolution\|resolution]] 0.96Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kcc\|1kcc]], [[1kcd\|1kcd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kcc\|1kcc]], [[1kcd\|1kcd]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [http://pdbe.org/1k5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [http://www.ebi.ac.uk/pdbsum/1k5c 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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [http://pdbe.org/1k5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [http://www.ebi.ac.uk/pdbsum/1k5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5c ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/1k5c_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/1k5c_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 16:44, 7 February 2016

OCA — Sun, 07 Feb 2016 16:44:21 GMT

←Older revision		Revision as of 16:44, 7 February 2016
Line 16:		Line 16:
	<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=1k5c ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:21, 10 September 2015

OCA — Thu, 10 Sep 2015 03:21:11 GMT

←Older revision		Revision as of 03:21, 10 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kcc\|1kcc]], [[1kcd\|1kcd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kcc\|1kcc]], [[1kcd\|1kcd]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [http://www.ebi.ac.uk/pdbsum/1k5c 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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [http://pdbe.org/1k5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [http://www.ebi.ac.uk/pdbsum/1k5c PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1k5c" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:37, 5 January 2015

OCA — Mon, 05 Jan 2015 16:37:34 GMT

←Older revision		Revision as of 16:37, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K5C FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K5C FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kcc\|1kcc]], [[1kcd\|1kcd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kcc\|1kcc]], [[1kcd\|1kcd]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [http://www.ebi.ac.uk/pdbsum/1k5c 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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [http://www.ebi.ac.uk/pdbsum/1k5c 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 32:		Line 32:
	[[Category: Chondrostereum purpureum]]		[[Category: Chondrostereum purpureum]]
	[[Category: Polygalacturonase]]		[[Category: Polygalacturonase]]
-	[[Category: Kato, H.]]	+	[[Category: Kato, H]]
-	[[Category: Miyairi, K.]]	+	[[Category: Miyairi, K]]
-	[[Category: Nakatsu, T.]]	+	[[Category: Nakatsu, T]]
-	[[Category: Okuno, T.]]	+	[[Category: Okuno, T]]
-	[[Category: Shimizu, T.]]	+	[[Category: Shimizu, T]]
	[[Category: Beta helical structure]]		[[Category: Beta helical structure]]
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Silver-leaf inducing substance]]		[[Category: Silver-leaf inducing substance]]

OCA at 14:09, 28 September 2014

OCA — Sun, 28 Sep 2014 14:09:35 GMT

←Older revision		Revision as of 14:09, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1k5c.~~png~~\|~~left~~\|200px]]	+	==Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution==
		+	<StructureSection load='1k5c' size='340' side='right' caption='[[1k5c]], [[Resolution\|resolution]] 0.96Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K5C FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kcc\|1kcc]], [[1kcd\|1kcd]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </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=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [http://www.ebi.ac.uk/pdbsum/1k5c 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/k5/1k5c_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 ==
		+	Crystal structures of endopolygalacturonase from Stereum purpureum were solved in native and two galacturonic acid complex states at atomic resolution. Endopolygalacturonase catalyzes the hydrolysis of alpha-1,4-glycosidic linkage of polygalacturonate in pectin. The native structure was determined by the multiple wavelength anomalous dispersion method and was refined anisotropically with SHELXL-97, with an R factor of 11.4% and an R(free) factor of 14.0% at 0.96 A resolution. The enzyme folds into a right-handed parallel beta-helix with 10 complete turns. The crystal structures of its binary complex with one D-galacturonate and its ternary complex with two D-galacturonates were also determined to identify the substrate binding site at 1.0 and 1.15 A resolutions, respectively. In the binary complex, one beta-D-galactopyranuronate was found in the +1 subsite, thus proving the strong affinity of the +1 subsite expected from the bond cleavage frequency on oligogalacturonates. In the ternary complex, an additional beta-D-galactofuranuronate was found in the -1 subsite. In both subsites, the recognition of the galacturonate carboxy group is important in galacturonate binding. In the +1 subsite, the carboxy group interacts with three basic residues, His195, Arg226, and Lys228, which were conserved in all endopolygalacturonases. In the -1 subsite, the unique nonprolyl cis-peptide bond is believed to be involved in binding the carboxy group of the substrate. The active site architecture of the complexes provides insight into the mechanism of inverting glycosyl hydrolases and also sheds light on the basis of the differences between the family 28 and the other inverting glycosyl hydrolases.

-	~~{{STRUCTURE_1k5c\| PDB=1k5c \| SCENE= }}~~	+	Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.,Shimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H Biochemistry. 2002 May 28;41(21):6651-9. PMID:12022868<ref>PMID:12022868</ref>

-	~~===Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12022868}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1k5c]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012022868<~~/~~ref~~><~~ref group="xtra">PMID:018754631</ref><references group="xtra"~~/>	+
	[[Category: Chondrostereum purpureum]]		[[Category: Chondrostereum purpureum]]
	[[Category: Polygalacturonase]]		[[Category: Polygalacturonase]]

OCA: Protected "1k5c" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 20:53:52 GMT

Protected "1k5c" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:53, 5 December 2012

OCA at 20:53, 5 December 2012

OCA — Wed, 05 Dec 2012 20:53:49 GMT

←Older revision		Revision as of 20:53, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1k5c.png\|left\|200px]]		[[Image:1k5c.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1k5c", 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_1k5c\| PDB=1k5c \| SCENE= }}		{{STRUCTURE_1k5c\| PDB=1k5c \| SCENE= }}

	===Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution===		===Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12022868}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12022868 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12022868}}		{{ABSTRACT_PUBMED_12022868}}

	==About this Structure==		==About this Structure==
-	~~1K5C~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA].	+	[[1k5c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12022868~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012022868</ref><ref group="xtra">PMID:018754631</ref><references group="xtra"/>
	[[Category: Chondrostereum purpureum]]		[[Category: Chondrostereum purpureum]]
	[[Category: Polygalacturonase]]		[[Category: Polygalacturonase]]
Line 33:		Line 21:
	[[Category: Beta helical structure]]		[[Category: Beta helical structure]]
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
	[[Category: Silver-leaf inducing substance]]		[[Category: Silver-leaf inducing substance]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:12:11 2009''