1xrs - Revision history

OCA at 07:57, 15 May 2024

OCA — Wed, 15 May 2024 07:57:26 GMT

←Older revision		Revision as of 07:57, 15 May 2024
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	<StructureSection load='1xrs' size='340' side='right'caption='[[1xrs]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xrs' size='340' side='right'caption='[[1xrs]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_12662 Atcc 12662~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XRS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetoanaerobium_sticklandii Acetoanaerobium sticklandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XRS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=5AD:5~~-~~DEOXYADENOSINE'>5AD</scene>~~, ~~<scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=1511 ATCC 12662])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Beta~~-~~lysine_5,6-aminomutase Beta-lysine~~ 5,6-~~aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3]~~ </~~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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [https://pdbe.org/1xrs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [https://www.ebi.ac.uk/pdbsum/1xrs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrs ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [~~http~~://pdbe.org/1xrs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xrs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrs ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~KAMDD_CLOSD KAMDD_CLOSD]~~] Catalyzes the ~~1,2-~~migration of the D-lysine epsilon amino group to the delta carbon ~~with concomitant reverse migration of a hydrogen atom~~ to produce 2,5-~~diaminohexanoic acid~~.<ref>PMID:10617592</ref> [[http://www.uniprot.org/uniprot/KAMED_CLOSD KAMED_CLOSD]] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.<ref>PMID:~~10617592~~</ref>	+	[https://www.uniprot.org/uniprot/KAMD_ACESD KAMD_ACESD] Catalyzes the migration of the L-beta-lysine and D-lysine epsilon amino group to the delta carbon to produce 3,5-diaminohexanoate and 2,5-diaminohexanoate, respectively.<ref>PMID:10617592</ref> <ref>PMID:11318641</ref>
	== 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: ~~Atcc 12662]]~~	+	[[Category: Acetoanaerobium sticklandii]]
-	~~[[Category: Beta-lysine 5,6-aminomutase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Behshad, E]]	+	[[Category: Behshad E]]
-	[[Category: Berkovitch, F]]	+	[[Category: Berkovitch F]]
-	[[Category: Drennan~~, C L~~]]	+	[[Category: Drennan CL]]
-	[[Category: Enns~~, E A~~]]	+	[[Category: Enns EA]]
-	[[Category: Frey~~, P A~~]]	+	[[Category: Frey PA]]
-	[[Category: Tang~~, K H]]~~	+	[[Category: Tang KH]]
-	~~[[Category: 5'-deoxyadenosine]]~~	+
-	~~[[Category: Adenosylcobalamin]]~~	+
-	~~[[Category: B12]]~~	+
-	~~[[Category: Cobalamin]]~~	+
-	~~[[Category: Conformational change]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Mutase]]~~	+
-	~~[[Category: Plp]]~~	+
-	~~[[Category: Radical]]~~	+
-	~~[[Category: Rossmann domain]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 10:17, 6 January 2021

OCA — Wed, 06 Jan 2021 10:17:39 GMT

←Older revision		Revision as of 10:17, 6 January 2021
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	==Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine==		==Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine==
-	<StructureSection load='1xrs' size='340' side='right' caption='[[1xrs]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1xrs' size='340' side='right'caption='[[1xrs]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12662 Atcc 12662]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XRS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12662 Atcc 12662]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XRS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://pdbe.org/1xrs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrs ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://pdbe.org/1xrs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/xr/1xrs_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xr/1xrs_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 32:		Line 32:

	==See Also==		==See Also==
-	*[[Aminomutase\|Aminomutase]]	+	*[[Aminomutase 3D structures\|Aminomutase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	[[Category: Atcc 12662]]		[[Category: Atcc 12662]]
	[[Category: Beta-lysine 5,6-aminomutase]]		[[Category: Beta-lysine 5,6-aminomutase]]
		+	[[Category: Large Structures]]
	[[Category: Behshad, E]]		[[Category: Behshad, E]]
	[[Category: Berkovitch, F]]		[[Category: Berkovitch, F]]

OCA at 07:56, 12 October 2017

OCA — Thu, 12 Oct 2017 07:56:54 GMT

←Older revision		Revision as of 07:56, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine==		==Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine==
	<StructureSection load='1xrs' size='340' side='right' caption='[[1xrs]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xrs' size='340' side='right' caption='[[1xrs]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://pdbe.org/1xrs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs 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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://pdbe.org/1xrs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=1xrs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 1xrs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1xrs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminomutase\|Aminomutase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:32, 11 September 2015

OCA — Fri, 11 Sep 2015 13:32:40 GMT

←Older revision		Revision as of 13:32, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1xrs' size='340' side='right' caption='[[1xrs]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xrs' size='340' side='right' caption='[[1xrs]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~[clostridium]_sticklandii [clostridium] sticklandii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XRS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12662 Atcc 12662]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XRS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ~~[Clostridium] sticklandii~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 ATCC 12662])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs 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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://pdbe.org/1xrs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~Q9ZFE6_CLOST Q9ZFE6_CLOST~~]] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.<ref>PMID:10617592</ref> [[http://www.uniprot.org/uniprot/~~Q9ZFE5_CLOST Q9ZFE5_CLOST~~]] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.<ref>PMID:10617592</ref>	+	[[http://www.uniprot.org/uniprot/KAMDD_CLOSD KAMDD_CLOSD]] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.<ref>PMID:10617592</ref> [[http://www.uniprot.org/uniprot/KAMED_CLOSD KAMED_CLOSD]] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.<ref>PMID:10617592</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	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 1xrs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12662]]
	[[Category: Beta-lysine 5,6-aminomutase]]		[[Category: Beta-lysine 5,6-aminomutase]]
	[[Category: Behshad, E]]		[[Category: Behshad, E]]

OCA at 17:07, 25 December 2014

OCA — Thu, 25 Dec 2014 17:07:41 GMT

←Older revision		Revision as of 17:07, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/[clostridium]_sticklandii [clostridium] sticklandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XRS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/[clostridium]_sticklandii [clostridium] sticklandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XRS FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 [Clostridium] sticklandii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 [Clostridium] sticklandii])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs 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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q9ZFE6_CLOST Q9ZFE6_CLOST]] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.<ref>PMID:10617592</ref> [[http://www.uniprot.org/uniprot/Q9ZFE5_CLOST Q9ZFE5_CLOST]] Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.<ref>PMID:10617592</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lysine 5,6-aminomutase]]		[[Category: Beta-lysine 5,6-aminomutase]]
-	[[Category: Behshad, E.]]	+	[[Category: Behshad, E]]
-	[[Category: Berkovitch, F.]]	+	[[Category: Berkovitch, F]]
-	[[Category: Drennan, C L.]]	+	[[Category: Drennan, C L]]
-	[[Category: Enns, E A.]]	+	[[Category: Enns, E A]]
-	[[Category: Frey, P A.]]	+	[[Category: Frey, P A]]
-	[[Category: Tang, K H.]]	+	[[Category: Tang, K H]]
	[[Category: 5'-deoxyadenosine]]		[[Category: 5'-deoxyadenosine]]
	[[Category: Adenosylcobalamin]]		[[Category: Adenosylcobalamin]]

OCA at 22:12, 28 September 2014

OCA — Sun, 28 Sep 2014 22:12:57 GMT

←Older revision		Revision as of 22:12, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xrs.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine==
		+	<StructureSection load='1xrs' size='340' side='right' caption='[[1xrs]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/[clostridium]_sticklandii [clostridium] sticklandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XRS FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KamDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1511 [Clostridium] sticklandii])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lysine_5,6-aminomutase Beta-lysine 5,6-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.3 5.4.3.3] </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=1xrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xrs RCSB], [http://www.ebi.ac.uk/pdbsum/1xrs 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/xr/1xrs_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 ==
		+	Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5'-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-beta-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this structure, a Rossmann domain covalently binds pyridoxal-5'-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, approximately 25 A from the active site. In this mode of pyridoxal-5'-phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5'-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.

-	~~{{STRUCTURE_1xrs\| PDB=1xrs \| SCENE= }}~~	+	A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.,Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15870-5. Epub 2004 Oct 28. PMID:15514022<ref>PMID:15514022</ref>

-	~~===Crystal structure of Lysine 5~~,~~6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15514022}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1xrs]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/[clostridium]_sticklandii [clostridium] sticklandii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015514022<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Beta-lysine 5,6-aminomutase]]		[[Category: Beta-lysine 5,6-aminomutase]]
	[[Category: Behshad, E.]]		[[Category: Behshad, E.]]

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

OCA — Wed, 24 Oct 2012 06:30:05 GMT

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

←Older revision

Revision as of 06:30, 24 October 2012

OCA at 06:30, 24 October 2012

OCA — Wed, 24 Oct 2012 06:30:03 GMT

←Older revision		Revision as of 06:30, 24 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xrs.png\|left\|200px]]		[[Image:1xrs.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xrs", 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_1xrs\| PDB=1xrs \| SCENE= }}		{{STRUCTURE_1xrs\| PDB=1xrs \| SCENE= }}

	===Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine===		===Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15514022}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15514022 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15514022}}		{{ABSTRACT_PUBMED_15514022}}

	==About this Structure==		==About this Structure==
-	~~1XRS~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Clostridium_sticklandii Clostridium~~ sticklandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA].	+	[[1xrs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/[clostridium]_sticklandii [clostridium] sticklandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15514022~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015514022</ref><references group="xtra"/>
	[[Category: Beta-lysine 5,6-aminomutase]]		[[Category: Beta-lysine 5,6-aminomutase]]
-	[[Category: Clostridium sticklandii]]
	[[Category: Behshad, E.]]		[[Category: Behshad, E.]]
	[[Category: Berkovitch, F.]]		[[Category: Berkovitch, F.]]
Line 37:		Line 24:
	[[Category: Cobalamin]]		[[Category: Cobalamin]]
	[[Category: Conformational change]]		[[Category: Conformational change]]
		+	[[Category: Isomerase]]
	[[Category: Mutase]]		[[Category: Mutase]]
	[[Category: Plp]]		[[Category: Plp]]
Line 42:		Line 30:
	[[Category: Rossmann domain]]		[[Category: Rossmann domain]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:23:51 2009''

OCA at 21:23, 17 February 2009

OCA — Tue, 17 Feb 2009 21:23:55 GMT

←Older revision		Revision as of 21:23, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1XRS is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Clostridium_sticklandii Clostridium sticklandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA].	+	1XRS is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Clostridium_sticklandii Clostridium sticklandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRS OCA].

	==Reference==		==Reference==
-	A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase., Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL, Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15870-5. Epub 2004 Oct 28. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15514022 15514022]~~	+	<ref group="xtra">PMID:15514022</ref><references group="xtra"/>
	[[Category: Beta-lysine 5,6-aminomutase]]		[[Category: Beta-lysine 5,6-aminomutase]]
	[[Category: Clostridium sticklandii]]		[[Category: Clostridium sticklandii]]
-	[[Category: Protein complex]]
	[[Category: Behshad, E.]]		[[Category: Behshad, E.]]
	[[Category: Berkovitch, F.]]		[[Category: Berkovitch, F.]]
Line 44:		Line 43:
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 06~~:55:~~52 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:23:51 2009''

OCA at 03:55, 29 July 2008

OCA — Tue, 29 Jul 2008 03:55:57 GMT

←Older revision		Revision as of 03:55, 29 July 2008
Line 1:		Line 1:
-	[[Image:1xrs.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1xrs.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1xrs\| PDB=1xrs \| SCENE= }}		{{STRUCTURE_1xrs\| PDB=1xrs \| SCENE= }}

-	~~'''~~Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine~~'''~~	+	===Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine===


-	~~==Overview==~~	+	<!--
-	~~Lysine 5,6~~-~~aminomutase is an adenosylcobalamin and pyridoxal~~-5'-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-beta-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this ~~structure~~, ~~a Rossmann domain covalently binds pyridoxal-5'-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain~~, ~~while simultaneously positioning~~ the ~~other cofactor, adenosylcobalamin, approximately 25 A from~~ the ~~active site~~. ~~In this mode of pyridoxal-5'-phosphate binding~~, the ~~cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain~~. ~~Upon substrate binding and transaldimination of the lysine~~-~~144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal~~-5'-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.	+	The line below this paragraph, {{ABSTRACT_PUBMED_15514022}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15514022 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15514022}}

	==About this Structure==		==About this Structure==
Line 39:		Line 43:
	[[Category: Rossmann domain]]		[[Category: Rossmann domain]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 15~~:25:44 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:55:52 2008''