2zm8 - Revision history

OCA at 13:43, 1 November 2023

OCA — Wed, 01 Nov 2023 13:43:22 GMT

←Older revision		Revision as of 13:43, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2zm8' size='340' side='right'caption='[[2zm8]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2zm8' size='340' side='right'caption='[[2zm8]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zm8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"corynebacterium_creatinovorans"_dubos_and_miller_1937 "corynebacterium creatinovorans" dubos and miller 1937~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZM8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zm8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZM8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.55Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wyb\|1wyb]], [[1wyc\|1wyc]], [[2dcf\|2dcf]], [[2e8i\|2e8i]], [[2zm7\|2zm7]], [[2zm9\|2zm9]], [[2zma\|2zma]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37931 "Corynebacterium creatinovorans" Dubos and Miller 1937])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [https://pdbe.org/2zm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [https://www.ebi.ac.uk/pdbsum/2zm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm8 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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [https://pdbe.org/2zm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [https://www.ebi.ac.uk/pdbsum/2zm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NYLB2_FLASK NYLB2_FLASK] Involved in nylon oligomer degradation.<ref>PMID:6389532</ref> <ref>PMID:6646204</ref> [https://www.uniprot.org/uniprot/NYLB_FLASK NYLB_FLASK]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Corynebacterium creatinovorans dubos and miller 1937]]~~	+	[[Category: Flavobacterium sp]]
-	~~[[Category: 6-aminohexanoate-dimer hydrolase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Higuchi, Y]]	+	[[Category: Higuchi Y]]
-	[[Category: Kato, D]]	+	[[Category: Kato D]]
-	[[Category: Kawashima, Y]]	+	[[Category: Kawashima Y]]
-	[[Category: Negoro, S]]	+	[[Category: Negoro S]]
-	[[Category: Ohki, T]]	+	[[Category: Ohki T]]
-	[[Category: Shibata, N]]	+	[[Category: Shibata N]]
-	[[Category: Takeo, M]]	+	[[Category: Takeo M]]
-	~~[[Category: Alpha-beta]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nylon degradation~~]]	+

OCA at 07:17, 10 November 2021

OCA — Wed, 10 Nov 2021 07:17:47 GMT

←Older revision		Revision as of 07:17, 10 November 2021
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	==Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer==		==Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer==
-	<StructureSection load='2zm8' size='340' side='right' caption='[[2zm8]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='2zm8' size='340' side='right'caption='[[2zm8]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zm8]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Flask Flask~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZM8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zm8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"corynebacterium_creatinovorans"_dubos_and_miller_1937 "corynebacterium creatinovorans" dubos and miller 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZM8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyb\|1wyb]], [[1wyc\|1wyc]], [[2dcf\|2dcf]], [[2e8i\|2e8i]], [[2zm7\|2zm7]], [[2zm9\|2zm9]], [[2zma\|2zma]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wyb\|1wyb]], [[1wyc\|1wyc]], [[2dcf\|2dcf]], [[2e8i\|2e8i]], [[2zm7\|2zm7]], [[2zm9\|2zm9]], [[2zma\|2zma]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~261 FLASK~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37931 "Corynebacterium creatinovorans" Dubos and Miller 1937])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [~~http~~://pdbe.org/2zm8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zm8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm8 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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [https://pdbe.org/2zm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [https://www.ebi.ac.uk/pdbsum/2zm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm8 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zm/2zm8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zm/2zm8_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>
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[6-aminohexanoate-dimer hydrolase\|6-aminohexanoate-dimer hydrolase]]	+	*[[6-aminohexanoate-dimer hydrolase 3D structures\|6-aminohexanoate-dimer hydrolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Corynebacterium creatinovorans dubos and miller 1937]]
	[[Category: 6-aminohexanoate-dimer hydrolase]]		[[Category: 6-aminohexanoate-dimer hydrolase]]
-	[[Category: ~~Flask~~]]	+	[[Category: Large Structures]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Kato, D]]		[[Category: Kato, D]]

OCA at 11:25, 7 October 2017

OCA — Sat, 07 Oct 2017 11:25:37 GMT

←Older revision		Revision as of 11:25, 7 October 2017
Line 1:		Line 1:
		+
	==Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer==		==Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer==
	<StructureSection load='2zm8' size='340' side='right' caption='[[2zm8]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2zm8' size='340' side='right' caption='[[2zm8]], [[Resolution\|resolution]] 1.55Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=261 FLASK])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=261 FLASK])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [http://pdbe.org/2zm8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [http://www.ebi.ac.uk/pdbsum/2zm8 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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [http://pdbe.org/2zm8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [http://www.ebi.ac.uk/pdbsum/2zm8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm8 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 01:40, 9 February 2016

OCA — Tue, 09 Feb 2016 01:40:51 GMT

←Older revision		Revision as of 01:40, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2zm8' size='340' side='right' caption='[[2zm8]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2zm8' size='340' side='right' caption='[[2zm8]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Flavobacterium_sp. Flavobacterium sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZM8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flask Flask]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZM8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyb\|1wyb]], [[1wyc\|1wyc]], [[2dcf\|2dcf]], [[2e8i\|2e8i]], [[2zm7\|2zm7]], [[2zm9\|2zm9]], [[2zma\|2zma]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyb\|1wyb]], [[1wyc\|1wyc]], [[2dcf\|2dcf]], [[2e8i\|2e8i]], [[2zm7\|2zm7]], [[2zm9\|2zm9]], [[2zma\|2zma]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~239 Flavobacterium sp.~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=261 FLASK])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [http://www.ebi.ac.uk/pdbsum/2zm8 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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [http://pdbe.org/2zm8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [http://www.ebi.ac.uk/pdbsum/2zm8 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 17:
	<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=2zm8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	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 2zm8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: 6-aminohexanoate-dimer hydrolase]]		[[Category: 6-aminohexanoate-dimer hydrolase]]
-	[[Category: ~~Flavobacterium sp~~]]	+	[[Category: Flask]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Kato, D]]		[[Category: Kato, D]]

OCA at 09:41, 20 January 2015

OCA — Tue, 20 Jan 2015 09:41:34 GMT

←Older revision		Revision as of 09:41, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZM8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZM8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyb\|1wyb]], [[1wyc\|1wyc]], [[2dcf\|2dcf]], [[2e8i\|2e8i]], [[2zm7\|2zm7]], [[2zm9\|2zm9]], [[2zma\|2zma]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyb\|1wyb]], [[1wyc\|1wyc]], [[2dcf\|2dcf]], [[2e8i\|2e8i]], [[2zm7\|2zm7]], [[2zm9\|2zm9]], [[2zma\|2zma]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=239 Flavobacterium sp.])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=239 Flavobacterium sp.])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [http://www.ebi.ac.uk/pdbsum/2zm8 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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [http://www.ebi.ac.uk/pdbsum/2zm8 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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: 6-aminohexanoate-dimer hydrolase]]		[[Category: 6-aminohexanoate-dimer hydrolase]]
-	[[Category: Flavobacterium sp.]]	+	[[Category: Flavobacterium sp]]
-	[[Category: Higuchi, Y.]]	+	[[Category: Higuchi, Y]]
-	[[Category: Kato, D.]]	+	[[Category: Kato, D]]
-	[[Category: Kawashima, Y.]]	+	[[Category: Kawashima, Y]]
-	[[Category: Negoro, S.]]	+	[[Category: Negoro, S]]
-	[[Category: Ohki, T.]]	+	[[Category: Ohki, T]]
-	[[Category: Shibata, N.]]	+	[[Category: Shibata, N]]
-	[[Category: Takeo, M.]]	+	[[Category: Takeo, M]]
	[[Category: Alpha-beta]]		[[Category: Alpha-beta]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nylon degradation]]		[[Category: Nylon degradation]]

OCA at 05:36, 2 October 2014

OCA — Thu, 02 Oct 2014 05:36:30 GMT

←Older revision		Revision as of 05:36, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2zm8.~~png~~\|~~left~~\|200px]]	+	==Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer==
		+	<StructureSection load='2zm8' size='340' side='right' caption='[[2zm8]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZM8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wyb\|1wyb]], [[1wyc\|1wyc]], [[2dcf\|2dcf]], [[2e8i\|2e8i]], [[2zm7\|2zm7]], [[2zm9\|2zm9]], [[2zma\|2zma]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=239 Flavobacterium sp.])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </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=2zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zm8 RCSB], [http://www.ebi.ac.uk/pdbsum/2zm8 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/zm/2zm8_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 ==
		+	Promiscuous 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity originally obtained in a carboxylesterase with a beta-lactamase fold was enhanced about 80-fold by directed evolution using error-prone PCR and DNA shuffling. Kinetic studies of the mutant enzyme (Hyb-S4M94) demonstrated that the enzyme had acquired an increased affinity (K(m) = 15 mM) and turnover (k(cat) = 3.1 s(-1)) for Ald, and that a catalytic center suitable for nylon-6 byproduct hydrolysis had been generated. Construction of various mutant enzymes revealed that the enhanced activity in the newly evolved enzyme is due to the substitutions R187S/F264C/D370Y. Crystal structures of Hyb-S4M94 with bound substrate suggested that catalytic function for Ald was improved by hydrogen-bonding/hydrophobic interactions between the Ald--COOH and Tyr370, a hydrogen-bonding network from Ser187 to Ald--NH(3) (+), and interaction between Ald--NH(3) (+) and Gln27-O(epsilon) derived from another subunit in the homo-dimeric structure. In wild-type Ald-hydrolase (NylB), Ald-hydrolytic activity is thought to be optimized by the substitutions G181D/H266N, which improve an electrostatic interaction with Ald--NH(3) (+) (Kawashima et al., FEBS J 2009; 276:2547-2556). We propose here that there exist at least two alternative modes for optimizing the Ald-hydrolytic activity of a carboxylesterase with a beta-lactamase fold.

-	~~{{STRUCTURE_2zm8\| PDB=2zm8 \| SCENE= }}~~	+	Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase.,Ohki T, Shibata N, Higuchi Y, Kawashima Y, Takeo M, Kato D, Negoro S Protein Sci. 2009 Aug;18(8):1662-73. PMID:19521995<ref>PMID:19521995</ref>

-	~~===Structure of 6-Aminohexanoate-dimer Hydrolase~~, ~~S112A~~/~~D370Y Mutant Complexed with 6-Aminohexanoate-dimer===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_19521995}}~~	+	==See Also==
-		+	*[[6-aminohexanoate-dimer hydrolase\|6-aminohexanoate-dimer hydrolase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2zm8~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:019521995<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 6-aminohexanoate-dimer hydrolase]]		[[Category: 6-aminohexanoate-dimer hydrolase]]
	[[Category: Flavobacterium sp.]]		[[Category: Flavobacterium sp.]]

OCA: Protected "2zm8" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 18:59:27 GMT

Protected "2zm8" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:59, 7 January 2013

OCA at 18:59, 7 January 2013

OCA — Mon, 07 Jan 2013 18:59:23 GMT

←Older revision		Revision as of 18:59, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2zm8.png\|left\|200px]]		[[Image:2zm8.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zm8", 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_2zm8\| PDB=2zm8 \| SCENE= }}		{{STRUCTURE_2zm8\| PDB=2zm8 \| SCENE= }}

	===Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer===		===Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19521995}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19521995 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19521995}}		{{ABSTRACT_PUBMED_19521995}}

	==About this Structure==		==About this Structure==
-	~~2ZM8~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA].	+	[[2zm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19521995~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019521995</ref><references group="xtra"/>
	[[Category: 6-aminohexanoate-dimer hydrolase]]		[[Category: 6-aminohexanoate-dimer hydrolase]]
	[[Category: Flavobacterium sp.]]		[[Category: Flavobacterium sp.]]
Line 36:		Line 24:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nylon degradation]]		[[Category: Nylon degradation]]
-	[[Category: Plasmid]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 6 08:58:07 2010''

OCA at 06:58, 6 January 2010

OCA — Wed, 06 Jan 2010 06:58:08 GMT

←Older revision		Revision as of 06:58, 6 January 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:2zm8.~~jpg~~\|left\|200px]]	+	[[Image:2zm8.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer===		===Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19521995}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19521995 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19521995}}

	==About this Structure==		==About this Structure==
	2ZM8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA].		2ZM8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19521995</ref><references group="xtra"/>
	[[Category: 6-aminohexanoate-dimer hydrolase]]		[[Category: 6-aminohexanoate-dimer hydrolase]]
	[[Category: Flavobacterium sp.]]		[[Category: Flavobacterium sp.]]
Line 29:		Line 38:
	[[Category: Plasmid]]		[[Category: Plasmid]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr 15 10~~:25:~~43 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 6 08:58:07 2010''

OCA at 07:25, 15 April 2009

OCA — Wed, 15 Apr 2009 07:25:46 GMT

←Older revision		Revision as of 07:25, 15 April 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:2zm8.jpg\|left\|200px]]

-	The ~~entry 2zm8~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2zm8", 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_2zm8\| PDB=2zm8 \| SCENE= }}

-	~~Authors: Ohki~~, ~~T., Shibata, N., Higuchi, Y., Kawashima, Y., Takeo, M., Kato, D., Negoro, S.~~	+	===Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer===

-	Description: Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/D370Y Mutant Complexed with 6-Aminohexanoate-dimer

		+	==About this Structure==
		+	2ZM8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM8 OCA].
		+	[[Category: 6-aminohexanoate-dimer hydrolase]]
		+	[[Category: Flavobacterium sp.]]
		+	[[Category: Higuchi, Y.]]
		+	[[Category: Kato, D.]]
		+	[[Category: Kawashima, Y.]]
		+	[[Category: Negoro, S.]]
		+	[[Category: Ohki, T.]]
		+	[[Category: Shibata, N.]]
		+	[[Category: Takeo, M.]]
		+	[[Category: Alpha-beta]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nylon degradation]]
		+	[[Category: Plasmid]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 11 09~~:21:~~51 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 15 10:25:43 2009''