2oo5 - Revision history

OCA at 10:45, 30 August 2023

OCA — Wed, 30 Aug 2023 10:45:39 GMT

←Older revision		Revision as of 10:45, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2oo5' size='340' side='right'caption='[[2oo5]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2oo5' size='340' side='right'caption='[[2oo5]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oo5]] 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=2OO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OO5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oo5]] 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=2OO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OO5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAP:NADP+NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TXD:1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>TXD</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]] 2.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1u2d\|1u2d]], [[1hzz\|1hzz]], [[2oor\|2oor]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TXD:1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>TXD</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>pntAA, nntA1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1085~~ "~~Dicrospirillum rubrum~~" ~~Enderlein 1925]), pntB, nntB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=1085 "Dicrospirillum rubrum" Enderlein 1925])</td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si~~-~~specific) NAD(P)(~~+~~) transhydrogenase (Re/Si-specific)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2]~~ </~~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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [https://pdbe.org/2oo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [https://www.ebi.ac.uk/pdbsum/2oo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oo5 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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [https://pdbe.org/2oo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [https://www.ebi.ac.uk/pdbsum/2oo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oo5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~PNTAA_RHORU PNTAA_RHORU]~~] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane ~~(By similarity)~~. [~~[https~~:~~//www.uniprot.org/uniprot/PNTB_RHORU PNTB_RHORU~~]~~] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity).~~	+	[https://www.uniprot.org/uniprot/PNTAA_RHORT PNTAA_RHORT] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane.[UniProtKB:P07001]
	== 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: ~~Bhakta, T~~]]	+	[[Category: Rhodospirillum rubrum]]
-	[[Category: ~~Jackson, J B~~]]	+	[[Category: Bhakta T]]
-	[[Category: ~~Oxidoreductase]]~~	+	[[Category: Jackson JB]]
-	~~[[Category: Rossmann fold~~]]	+

OCA at 13:01, 9 June 2021

OCA — Wed, 09 Jun 2021 13:01:31 GMT

←Older revision		Revision as of 13:01, 9 June 2021
Line 1:		Line 1:

	==Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex==		==Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex==
-	<StructureSection load='2oo5' size='340' side='right' caption='[[2oo5]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='2oo5' size='340' side='right'caption='[[2oo5]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oo5]] 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=2OO5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OO5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oo5]] 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=2OO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OO5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TXD:1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>TXD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TXD:1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>TXD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u2d\|1u2d]], [[1hzz\|1hzz]], [[2oor\|2oor]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1u2d\|1u2d]], [[1hzz\|1hzz]], [[2oor\|2oor]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925]), pntB, nntB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925]), pntB, nntB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [~~http~~://pdbe.org/2oo5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2oo5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2oo5 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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [https://pdbe.org/2oo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [https://www.ebi.ac.uk/pdbsum/2oo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oo5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PNTAA_RHORU PNTAA_RHORU]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity). [[~~http~~://www.uniprot.org/uniprot/PNTB_RHORU PNTB_RHORU]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity).	+	[[https://www.uniprot.org/uniprot/PNTAA_RHORU PNTAA_RHORU]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity). [[https://www.uniprot.org/uniprot/PNTB_RHORU PNTB_RHORU]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[NAD(P) transhydrogenase\|NAD(P) transhydrogenase]]	+	*[[NAD(P) transhydrogenase 3D structures\|NAD(P) transhydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Dicrospirillum rubrum enderlein 1925]]		[[Category: Dicrospirillum rubrum enderlein 1925]]
		+	[[Category: Large Structures]]
	[[Category: Bhakta, T]]		[[Category: Bhakta, T]]
	[[Category: Jackson, J B]]		[[Category: Jackson, J B]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

OCA at 07:33, 22 August 2018

OCA — Wed, 22 Aug 2018 07:33:48 GMT

←Older revision		Revision as of 07:33, 22 August 2018
Line 1:		Line 1:
		+
	==Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex==		==Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex==
	<StructureSection load='2oo5' size='340' side='right' caption='[[2oo5]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2oo5' size='340' side='right' caption='[[2oo5]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925]), pntB, nntB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925]), pntB, nntB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [http://pdbe.org/2oo5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [http://www.ebi.ac.uk/pdbsum/2oo5 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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [http://pdbe.org/2oo5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [http://www.ebi.ac.uk/pdbsum/2oo5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oo5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oo/2oo5_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oo/2oo5_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 19:41, 9 February 2016

OCA — Tue, 09 Feb 2016 19:41:35 GMT

←Older revision		Revision as of 19:41, 9 February 2016
Line 19:		Line 19:
	<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=2oo5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:26, 11 September 2015

OCA — Fri, 11 Sep 2015 01:26:36 GMT

←Older revision		Revision as of 01:26, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2oo5' size='340' side='right' caption='[[2oo5]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2oo5' size='340' side='right' caption='[[2oo5]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oo5]] 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=2OO5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OO5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oo5]] 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=2OO5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OO5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TXD:1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>TXD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TXD:1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>TXD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u2d\|1u2d]], [[1hzz\|1hzz]], [[2oor\|2oor]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u2d\|1u2d]], [[1hzz\|1hzz]], [[2oor\|2oor]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 ~~Rhodospirillum~~ rubrum]), pntB, nntB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 ~~Rhodospirillum~~ rubrum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925]), pntB, nntB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(AB-specific) NAD(P)(+) transhydrogenase (AB-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [http://www.ebi.ac.uk/pdbsum/2oo5 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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [http://pdbe.org/2oo5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [http://www.ebi.ac.uk/pdbsum/2oo5 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 2oo5" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhodospirillum~~ rubrum]]	+	[[Category: Dicrospirillum rubrum enderlein 1925]]
	[[Category: Bhakta, T]]		[[Category: Bhakta, T]]
	[[Category: Jackson, J B]]		[[Category: Jackson, J B]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

OCA at 09:06, 25 December 2014

OCA — Thu, 25 Dec 2014 09:06:22 GMT

←Older revision		Revision as of 09:06, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2oo5]] 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=2OO5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OO5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oo5]] 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=2OO5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OO5 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TXD:1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>TXD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TXD:1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>TXD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u2d\|1u2d]], [[1hzz\|1hzz]], [[2oor\|2oor]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u2d\|1u2d]], [[1hzz\|1hzz]], [[2oor\|2oor]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 Rhodospirillum rubrum]), pntB, nntB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 Rhodospirillum rubrum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 Rhodospirillum rubrum]), pntB, nntB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 Rhodospirillum rubrum])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(AB-specific) NAD(P)(+) transhydrogenase (AB-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(AB-specific) NAD(P)(+) transhydrogenase (AB-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [http://www.ebi.ac.uk/pdbsum/2oo5 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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [http://www.ebi.ac.uk/pdbsum/2oo5 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PNTAA_RHORU PNTAA_RHORU]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity). [[http://www.uniprot.org/uniprot/PNTB_RHORU PNTB_RHORU]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
-	[[Category: Bhakta, T.]]	+	[[Category: Bhakta, T]]
-	[[Category: Jackson, J B.]]	+	[[Category: Jackson, J B]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

OCA at 20:22, 30 September 2014

OCA — Tue, 30 Sep 2014 20:22:11 GMT

←Older revision		Revision as of 20:22, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2oo5.~~png~~\|~~left~~\|200px]]	+	==Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex==
		+	<StructureSection load='2oo5' size='340' side='right' caption='[[2oo5]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2oo5]] 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=2OO5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OO5 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TXD:1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>TXD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u2d\|1u2d]], [[1hzz\|1hzz]], [[2oor\|2oor]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 Rhodospirillum rubrum]), pntB, nntB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 Rhodospirillum rubrum])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(AB-specific) NAD(P)(+) transhydrogenase (AB-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </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=2oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oo5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oo5 RCSB], [http://www.ebi.ac.uk/pdbsum/2oo5 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/oo/2oo5_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 ==
		+	Transhydrogenase couples the redox reaction between NADH and NADP+ to proton translocation across a membrane. The enzyme comprises three components; dI binds NAD(H), dIII binds NADP(H), and dII spans the membrane. The 1,4,5,6-tetrahydro analogue of NADH (designated H2NADH) bound to isolated dI from Rhodospirillum rubrum transhydrogenase with similar affinity to the physiological nucleotide. Binding of either NADH or H2NADH led to closure of the dI mobile loop. The 1,4,5,6-tetrahydro analogue of NADPH (H2NADPH) bound very tightly to isolated R. rubrum dIII, but the rate constant for dissociation was greater than that for NADPH. The replacement of NADP+ on dIII either with H2NADPH or with NADPH caused a similar set of chemical shift alterations, signifying an equivalent conformational change. Despite similar binding properties to the natural nucleotides, neither H2NADH nor H2NADPH could serve as a hydride donor in transhydrogenation reactions. Mixtures of dI and dIII form dI2dIII1 complexes. The nucleotide charge distribution of complexes loaded either with H2NADH and NADP+ or with NAD+ and H2NADPH should more closely mimic the ground states for forward and reverse hydride transfer, respectively, than previously studied dead-end species. Crystal structures of such complexes at 2.6 and 2.3 A resolution are described. A transition state for hydride transfer between dihydronicotinamide and nicotinamide derivatives determined in ab initio quantum mechanical calculations resembles the organization of nucleotides in the transhydrogenase active site in the crystal structure. Molecular dynamics simulations of the enzyme indicate that the (dihydro)nicotinamide rings remain close to a ground state for hydride transfer throughout a 1.4 ns trajectory.

-	~~{{STRUCTURE_2oo5\| PDB=2oo5 \| SCENE= }}~~	+	Structures of the dI2dIII1 complex of proton-translocating transhydrogenase with bound, inactive analogues of NADH and NADPH reveal active site geometries.,Bhakta T, Whitehead SJ, Snaith JS, Dafforn TR, Wilkie J, Rajesh S, White SA, Jackson JB Biochemistry. 2007 Mar 20;46(11):3304-18. Epub 2007 Feb 27. PMID:17323922<ref>PMID:17323922</ref>

-	~~===Structure~~ of ~~transhydrogenase (dI~~.~~H2NADH)2(dIII~~.~~NADP+)1 asymmetric complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_17323922}}~~	+	==See Also==
-		+	*[[NAD(P) transhydrogenase\|NAD(P) transhydrogenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2oo5~~]] 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=2OO5 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:017323922<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
	[[Category: Bhakta, T.]]		[[Category: Bhakta, T.]]

OCA: Protected "2oo5" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 12:45:32 GMT

Protected "2oo5" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:45, 7 January 2013

OCA at 12:45, 7 January 2013

OCA — Mon, 07 Jan 2013 12:45:29 GMT

←Older revision		Revision as of 12:45, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2oo5.png\|left\|200px]]		[[Image:2oo5.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2oo5", 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_2oo5\| PDB=2oo5 \| SCENE= }}		{{STRUCTURE_2oo5\| PDB=2oo5 \| SCENE= }}

	===Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex===		===Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17323922}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17323922 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17323922}}		{{ABSTRACT_PUBMED_17323922}}

	==About this Structure==		==About this Structure==
-	~~2OO5~~ 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=2OO5 OCA].	+	[[2oo5]] 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=2OO5 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17323922~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017323922</ref><references group="xtra"/>
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
	[[Category: Bhakta, T.]]		[[Category: Bhakta, T.]]
	[[Category: Jackson, J B.]]		[[Category: Jackson, J B.]]
		+	[[Category: Oxidoreductase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:16:04 2009''

OCA at 10:16, 17 February 2009

OCA — Tue, 17 Feb 2009 10:16:04 GMT

←Older revision		Revision as of 10:16, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2OO5 is a ~~[[Protein complex]]~~ 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=2OO5 OCA].	+	2OO5 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=2OO5 OCA].

	==Reference==		==Reference==
-	Structures of the dI2dIII1 complex of proton-translocating transhydrogenase with bound, inactive analogues of NADH and NADPH reveal active site geometries., Bhakta T, Whitehead SJ, Snaith JS, Dafforn TR, Wilkie J, Rajesh S, White SA, Jackson JB, Biochemistry. 2007 Mar 20;46(11):3304-18. Epub 2007 Feb 27. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17323922 17323922]~~	+	<ref group="xtra">PMID:17323922</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
	[[Category: Bhakta, T.]]		[[Category: Bhakta, T.]]
Line 30:		Line 29:
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 16~~:33:04 ~~2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:16:04 2009''