2qjm - Revision history

OCA at 11:34, 30 August 2023

OCA — Wed, 30 Aug 2023 11:34:15 GMT

←Older revision		Revision as of 11:34, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2qjm' size='340' side='right'caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2qjm' size='340' side='right'caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_700278 Atcc 700278~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QJM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QJM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CS2:D~~-~~MANNONIC+ACID'>CS2</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2qjj\|2qjj]]~~, ~~[[2qjn\|2qjn]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [https://pdbe.org/2qjm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [https://www.ebi.ac.uk/pdbsum/2qjm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjm 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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [https://pdbe.org/2qjm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [https://www.ebi.ac.uk/pdbsum/2qjm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MAND_NOVAD MAND_NOVAD] Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).<ref>PMID:17944491</ref> <ref>PMID:24697546</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 700278]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Almo, S C~~]]	+	[[Category: Novosphingobium aromaticivorans]]
-	[[Category: ~~Fedorov, A A~~]]	+	[[Category: Almo SC]]
-	[[Category: Fedorov~~, E V~~]]	+	[[Category: Fedorov AA]]
-	[[Category: ~~Gerlt, J A~~]]	+	[[Category: Fedorov EV]]
-	[[Category: ~~Rakus, J F~~]]	+	[[Category: Gerlt JA]]
-	[[Category: ~~Vick, J E~~]]	+	[[Category: Rakus JF]]
-	[[Category: ~~D-mannonate dehydratase]]~~	+	[[Category: Vick JE]]
-	~~[[Category: Enolase superfamily]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 18:38, 20 October 2021

OCA — Wed, 20 Oct 2021 18:38:40 GMT

←Older revision		Revision as of 18:38, 20 October 2021
Line 3:		Line 3:
	<StructureSection load='2qjm' size='340' side='right'caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2qjm' size='340' side='right'caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_700278 Atcc 700278]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2QJM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_700278 Atcc 700278]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QJM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qjj\|2qjj]], [[2qjn\|2qjn]]</div></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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [~~http~~://pdbe.org/2qjm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qjm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjm 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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [https://pdbe.org/2qjm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [https://www.ebi.ac.uk/pdbsum/2qjm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:06, 10 June 2020

OCA — Wed, 10 Jun 2020 07:06:09 GMT

←Older revision		Revision as of 07:06, 10 June 2020
Line 1:		Line 1:

	==Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate==		==Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate==
-	<StructureSection load='2qjm' size='340' side='right' caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2qjm' size='340' side='right'caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700278 Atcc 700278]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QJM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700278 Atcc 700278]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2QJM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [http://pdbe.org/2qjm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [http://www.ebi.ac.uk/pdbsum/2qjm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjm 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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [http://pdbe.org/2qjm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [http://www.ebi.ac.uk/pdbsum/2qjm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:
	==See Also==		==See Also==
	*[[Mandelate racemase/muconate lactonizing enzyme\|Mandelate racemase/muconate lactonizing enzyme]]		*[[Mandelate racemase/muconate lactonizing enzyme\|Mandelate racemase/muconate lactonizing enzyme]]
		+	*[[Mandelate racemase/muconate lactonizing enzyme 3D structures\|Mandelate racemase/muconate lactonizing enzyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 700278]]		[[Category: Atcc 700278]]
		+	[[Category: Large Structures]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Fedorov, A A]]		[[Category: Fedorov, A A]]

OCA at 10:59, 5 September 2018

OCA — Wed, 05 Sep 2018 10:59:44 GMT

←Older revision		Revision as of 10:59, 5 September 2018
Line 1:		Line 1:
		+
	==Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate==		==Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate==
	<StructureSection load='2qjm' size='340' side='right' caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2qjm' size='340' side='right' caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [http://pdbe.org/2qjm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [http://www.ebi.ac.uk/pdbsum/2qjm 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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [http://pdbe.org/2qjm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [http://www.ebi.ac.uk/pdbsum/2qjm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qj/2qjm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qj/2qjm_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>
	</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=2qjm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 2qjm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2qjm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Mandelate racemase/muconate lactonizing enzyme\|Mandelate racemase/muconate lactonizing enzyme]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:08, 11 September 2015

OCA — Fri, 11 Sep 2015 09:08:57 GMT

←Older revision		Revision as of 09:08, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2qjm' size='340' side='right' caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2qjm' size='340' side='right' caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Novosphingobium_aromaticivorans Novosphingobium aromaticivorans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700278 Atcc 700278]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [http://www.ebi.ac.uk/pdbsum/2qjm 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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [http://pdbe.org/2qjm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [http://www.ebi.ac.uk/pdbsum/2qjm PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 2qjm" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Novosphingobium aromaticivorans~~]]	+	[[Category: Atcc 700278]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Fedorov, A A]]		[[Category: Fedorov, A A]]

OCA at 16:31, 19 January 2015

OCA — Mon, 19 Jan 2015 16:31:52 GMT

←Older revision		Revision as of 16:31, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [http://www.ebi.ac.uk/pdbsum/2qjm 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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [http://www.ebi.ac.uk/pdbsum/2qjm 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 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Novosphingobium aromaticivorans]]		[[Category: Novosphingobium aromaticivorans]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Fedorov, A A.]]	+	[[Category: Fedorov, A A]]
-	[[Category: Fedorov, E V.]]	+	[[Category: Fedorov, E V]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Rakus, J F.]]	+	[[Category: Rakus, J F]]
-	[[Category: Vick, J E.]]	+	[[Category: Vick, J E]]
	[[Category: D-mannonate dehydratase]]		[[Category: D-mannonate dehydratase]]
	[[Category: Enolase superfamily]]		[[Category: Enolase superfamily]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 19:18, 30 September 2014

OCA — Tue, 30 Sep 2014 19:18:52 GMT

←Older revision		Revision as of 19:18, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qjm.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate==
		+	<StructureSection load='2qjm' size='340' side='right' caption='[[2qjm]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QJM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qjj\|2qjj]], [[2qjn\|2qjn]]</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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [http://www.ebi.ac.uk/pdbsum/2qjm 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/qj/2qjm_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 ==
		+	The d-mannonate dehydratase (ManD) function was assigned to a group of orthologous proteins in the mechanistically diverse enolase superfamily by screening a library of acid sugars. Structures of the wild type ManD from Novosphingobium aromaticivorans were determined at pH 7.5 in the presence of Mg2+ and also in the presence of Mg2+ and the 2-keto-3-keto-d-gluconate dehydration product; the structure of the catalytically active K271E mutant was determined at pH 5.5 in the presence of the d-mannonate substrate. As previously observed in the structures of other members of the enolase superfamily, ManD contains two domains, an N-terminal alpha+beta capping domain and a (beta/alpha)7beta-barrel domain. The barrel domain contains the ligands for the essential Mg2+, Asp 210, Glu 236, and Glu 262, at the ends of the third, fourth, and fifth beta-strands of the barrel domain, respectively. However, the barrel domain lacks both the Lys acid/base catalyst at the end of the second beta-strand and the His-Asp dyad acid/base catalyst at the ends of the seventh and sixth beta-strands, respectively, that are found in many members of the superfamily. Instead, a hydrogen-bonded dyad of Tyr 159 in a loop following the second beta-strand and Arg 147 at the end of the second beta-strand are positioned to initiate the reaction by abstraction of the 2-proton. Both Tyr 159 and His 212, at the end of the third beta-strand, are positioned to facilitate both syn-dehydration and ketonization of the resulting enol intermediate to yield the 2-keto-3-keto-d-gluconate product with the observed retention of configuration. The identities and locations of these acid/base catalysts as well as of cationic amino acid residues that stabilize the enolate anion intermediate define a new structural strategy for catalysis (subgroup) in the mechanistically diverse enolase superfamily. With these differences, we provide additional evidence that the ligands for the essential Mg2+ are the only conserved residues in the enolase superfamily, establishing the primary functional importance of the Mg2+-assisted strategy for stabilizing the enolate anion intermediate.

-	~~{{STRUCTURE_2qjm\| PDB=2qjm \| SCENE= }}~~	+	Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans.,Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA Biochemistry. 2007 Nov 13;46(45):12896-908. Epub 2007 Oct 18. PMID:17944491<ref>PMID:17944491</ref>

-	~~===Crystal structure~~ of the ~~K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17944491}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2qjm]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017944491<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Novosphingobium aromaticivorans]]		[[Category: Novosphingobium aromaticivorans]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]

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

OCA — Mon, 07 Jan 2013 22:02:19 GMT

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

←Older revision

Revision as of 22:02, 7 January 2013

OCA at 22:02, 7 January 2013

OCA — Mon, 07 Jan 2013 22:02:15 GMT

←Older revision		Revision as of 22:02, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2qjm.png\|left\|200px]]		[[Image:2qjm.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qjm", 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_2qjm\| PDB=2qjm \| SCENE= }}		{{STRUCTURE_2qjm\| PDB=2qjm \| SCENE= }}

	===Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate===		===Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17944491}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17944491 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17944491}}		{{ABSTRACT_PUBMED_17944491}}

	==About this Structure==		==About this Structure==
-	~~2QJM~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA].	+	[[2qjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17944491~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017944491</ref><references group="xtra"/>
	[[Category: Novosphingobium aromaticivorans]]		[[Category: Novosphingobium aromaticivorans]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
Line 34:		Line 22:
	[[Category: Enolase superfamily]]		[[Category: Enolase superfamily]]
	[[Category: Lyase]]		[[Category: Lyase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:28:04 2009''

OCA at 16:28, 17 February 2009

OCA — Tue, 17 Feb 2009 16:28:07 GMT

←Older revision		Revision as of 16:28, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2QJM is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA].	+	2QJM is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA].

	==Reference==		==Reference==
-	Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans., Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA, Biochemistry. 2007 Nov 13;46(45):12896-908. Epub 2007 Oct 18. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17944491 17944491]~~	+	<ref group="xtra">PMID:17944491</ref><references group="xtra"/>
	[[Category: Novosphingobium aromaticivorans]]		[[Category: Novosphingobium aromaticivorans]]
-	[[Category: Single protein]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
	[[Category: Fedorov, A A.]]		[[Category: Fedorov, A A.]]
Line 36:		Line 35:
	[[Category: Lyase]]		[[Category: Lyase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 02~~:26:~~30 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:28:04 2009''