2woe - Revision history

OCA at 10:15, 9 May 2024

OCA — Thu, 09 May 2024 10:15:39 GMT

←Older revision		Revision as of 10:15, 9 May 2024
Line 3:		Line 3:
	<StructureSection load='2woe' size='340' side='right'caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2woe' size='340' side='right'caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"dicrospirillum_rubrum"_enderlein_1925 "dicrospirillum~~ rubrum~~" enderlein 1925~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WOE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 1.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2woc\|2woc]], [[2wod\|2wod]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [https://pdbe.org/2woe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [https://www.ebi.ac.uk/pdbsum/2woe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2woe 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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [https://pdbe.org/2woe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [https://www.ebi.ac.uk/pdbsum/2woe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2woe ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DRAG_RHORU DRAG_RHORU] Involved in the regulation of nitrogen fixation activity by the reversible ADP-ribosylation of one subunit of the homodimeric dinitrogenase reductase component of the nitrogenase enzyme complex. The ADP-ribosyltransferase (DraT) transfers the ADP-ribose group from NAD to dinitrogenase reductase. The ADP-ribose group is removed through the action of the ADP-ribosylglycohydrolase (DraG, this entry).
	== 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: Dicrospirillum rubrum enderlein 1925]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Berthold~~, C L~~]]	+	[[Category: Rhodospirillum rubrum]]
-	[[Category: Hogbom, M]]	+	[[Category: Berthold CL]]
-	[[Category: Nordlund, S]]	+	[[Category: Hogbom M]]
-	[[Category: Wang, H]]	+	[[Category: Nordlund S]]
-	~~[[Category: Adp-ribosylglycohydrolase]]~~	+	[[Category: Wang H]]
-	~~[[Category: Dimanganese]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mono-adp-ribosylhydrolase]]~~	+
-	~~[[Category: Nitrogen fixation~~]]	+

OCA at 11:12, 6 April 2022

OCA — Wed, 06 Apr 2022 11:12:18 GMT

←Older revision		Revision as of 11:12, 6 April 2022
Line 3:		Line 3:
	<StructureSection load='2woe' size='340' side='right'caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2woe' size='340' side='right'caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"dicrospirillum_rubrum"_enderlein_1925 "dicrospirillum rubrum" enderlein 1925]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2WOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"dicrospirillum_rubrum"_enderlein_1925 "dicrospirillum rubrum" enderlein 1925]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WOE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2woc\|2woc]], [[2wod\|2wod]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [~~http~~://pdbe.org/2woe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2woe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2woe 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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [https://pdbe.org/2woe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [https://www.ebi.ac.uk/pdbsum/2woe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2woe ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:59, 1 July 2020

OCA — Wed, 01 Jul 2020 08:59:26 GMT

←Older revision		Revision as of 08:59, 1 July 2020
Line 1:		Line 1:

	==Crystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose==		==Crystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose==
-	<StructureSection load='2woe' size='340' side='right' caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='2woe' size='340' side='right'caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"dicrospirillum_rubrum"_enderlein_1925 "dicrospirillum rubrum" enderlein 1925]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2WOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"dicrospirillum_rubrum"_enderlein_1925 "dicrospirillum rubrum" enderlein 1925]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2WOE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [http://pdbe.org/2woe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [http://www.ebi.ac.uk/pdbsum/2woe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2woe 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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [http://pdbe.org/2woe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [http://www.ebi.ac.uk/pdbsum/2woe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2woe ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Dicrospirillum rubrum enderlein 1925]]		[[Category: Dicrospirillum rubrum enderlein 1925]]
		+	[[Category: Large Structures]]
	[[Category: Berthold, C L]]		[[Category: Berthold, C L]]
	[[Category: Hogbom, M]]		[[Category: Hogbom, M]]

OCA at 08:56, 26 September 2018

OCA — Wed, 26 Sep 2018 08:56:09 GMT

←Older revision		Revision as of 08:56, 26 September 2018
Line 1:		Line 1:
-	==~~CRYSTAL STRUCTURE OF THE~~ D97N ~~VARIANT OF DINITROGENASE REDUCTASE~~-~~ACTIVATING GLYCOHYDROLASE~~ (DRAG) ~~FROM RHODOSPIRILLUM RUBRUM IN COMPLEX WITH~~ ADP-~~RIBOSE~~==	+
		+	==Crystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose==
	<StructureSection load='2woe' size='340' side='right' caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2woe' size='340' side='right' caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [http://pdbe.org/2woe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [http://www.ebi.ac.uk/pdbsum/2woe 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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [http://pdbe.org/2woe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [http://www.ebi.ac.uk/pdbsum/2woe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2woe ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wo/2woe_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wo/2woe_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 22:09, 7 February 2016

OCA — Sun, 07 Feb 2016 22:09:16 GMT

←Older revision		Revision as of 22:09, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='2woe' size='340' side='right' caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2woe' size='340' side='right' caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodospirillum_rubrum Rhodospirillum~~ rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"dicrospirillum_rubrum"_enderlein_1925 "dicrospirillum rubrum" enderlein 1925]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WOE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [http://www.ebi.ac.uk/pdbsum/2woe 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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [http://pdbe.org/2woe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [http://www.ebi.ac.uk/pdbsum/2woe PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2woe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2woe" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhodospirillum~~ rubrum]]	+	[[Category: Dicrospirillum rubrum enderlein 1925]]
	[[Category: Berthold, C L]]		[[Category: Berthold, C L]]
	[[Category: Hogbom, M]]		[[Category: Hogbom, M]]

OCA at 10:00, 20 January 2015

OCA — Tue, 20 Jan 2015 10:00:09 GMT

←Older revision		Revision as of 10:00, 20 January 2015
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
-	[[Category: Berthold, C L.]]	+	[[Category: Berthold, C L]]
-	[[Category: Hogbom, M.]]	+	[[Category: Hogbom, M]]
-	[[Category: Nordlund, S.]]	+	[[Category: Nordlund, S]]
-	[[Category: Wang, H.]]	+	[[Category: Wang, H]]
	[[Category: Adp-ribosylglycohydrolase]]		[[Category: Adp-ribosylglycohydrolase]]
	[[Category: Dimanganese]]		[[Category: Dimanganese]]

OCA at 05:49, 10 October 2014

OCA — Fri, 10 Oct 2014 05:49:17 GMT

←Older revision		Revision as of 05:49, 10 October 2014
Line 2:		Line 2:
	<StructureSection load='2woe' size='340' side='right' caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2woe' size='340' side='right' caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. <br>	+	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WOE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Glucokinase Glucokinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2~~.7.1~~.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [http://www.ebi.ac.uk/pdbsum/2woe 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=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [http://www.ebi.ac.uk/pdbsum/2woe 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 24:		Line 24:
	Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG.,Berthold CL, Wang H, Nordlund S, Hogbom M Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14247-52. Epub 2009 Aug 12. PMID:19706507<ref>PMID:19706507</ref>		Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG.,Berthold CL, Wang H, Nordlund S, Hogbom M Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14247-52. Epub 2009 Aug 12. PMID:19706507<ref>PMID:19706507</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==

OCA at 08:33, 7 May 2014

OCA — Wed, 07 May 2014 08:33:43 GMT

←Older revision		Revision as of 08:33, 7 May 2014
Line 1:		Line 1:
-	[[~~Image:~~2woe.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF THE D97N VARIANT OF DINITROGENASE REDUCTASE-ACTIVATING GLYCOHYDROLASE (DRAG) FROM RHODOSPIRILLUM RUBRUM IN COMPLEX WITH ADP-RIBOSE==
		+	<StructureSection load='2woe' size='340' side='right' caption='[[2woe]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2woe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2woc\|2woc]], [[2wod\|2wod]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2woe RCSB], [http://www.ebi.ac.uk/pdbsum/2woe 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/wo/2woe_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 ==
		+	ADP-ribosylation is a ubiquitous regulatory posttranslational modification involved in numerous key processes such as DNA repair, transcription, cell differentiation, apoptosis, and the pathogenic mechanism of certain bacterial toxins. Despite the importance of this reversible process, very little is known about the structure and mechanism of the hydrolases that catalyze removal of the ADP-ribose moiety. In the phototrophic bacterium Rhodospirillum rubrum, dinitrogenase reductase-activating glycohydrolase (DraG), a dimanganese enzyme that reversibly associates with the cell membrane, is a key player in the regulation of nitrogenase activity. DraG has long served as a model protein for ADP-ribosylhydrolases. Here, we present the crystal structure of DraG in the holo and ADP-ribose bound forms. We also present the structure of a reaction intermediate analogue and propose a detailed catalytic mechanism for protein de-ADP-ribosylation involving ring opening of the substrate ribose. In addition, the particular manganese coordination in DraG suggests a rationale for the enzyme's preference for manganese over magnesium, although not requiring a redox active metal for the reaction.

-	<!--	+	Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG.,Berthold CL, Wang H, Nordlund S, Hogbom M Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14247-52. Epub 2009 Aug 12. PMID:19706507<ref>PMID:19706507</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2woe"~~, ~~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_2woe\| PDB=2woe \| SCENE= }}~~	+

-	~~===CRYSTAL STRUCTURE OF THE D97N VARIANT OF DINITROGENASE REDUCTASE-ACTIVATING GLYCOHYDROLASE (DRAG) FROM RHODOSPIRILLUM RUBRUM IN COMPLEX WITH ADP-RIBOSE===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_19706507}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 19706507 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_19706507}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2woe]] is a 3 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019706507<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
	[[Category: Berthold, C L.]]		[[Category: Berthold, C L.]]

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

OCA — Wed, 24 Aug 2011 05:03:41 GMT

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

←Older revision

Revision as of 05:03, 24 August 2011

OCA at 05:03, 24 August 2011

OCA — Wed, 24 Aug 2011 05:03:40 GMT

←Older revision		Revision as of 05:03, 24 August 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2woe.png\|left\|200px]]		[[Image:2woe.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~2WOE~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA].	+	[[2woe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOE OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19706507~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019706507</ref><references group="xtra"/>
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
	[[Category: Berthold, C L.]]		[[Category: Berthold, C L.]]
Line 34:		Line 33:
	[[Category: Mono-adp-ribosylhydrolase]]		[[Category: Mono-adp-ribosylhydrolase]]
	[[Category: Nitrogen fixation]]		[[Category: Nitrogen fixation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 08:37:57 2009''