2fr8 - Revision history

OCA at 09:31, 30 August 2023

OCA — Wed, 30 Aug 2023 09:31:31 GMT

←Older revision		Revision as of 09:31, 30 August 2023
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	<StructureSection load='2fr8' size='340' side='right'caption='[[2fr8]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2fr8' size='340' side='right'caption='[[2fr8]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fr8]] 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=2FR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FR8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fr8]] 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=2FR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FR8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</scene>~~, ~~<scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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;'>[[1hzz\|1hzz]], [[1nm5\|1nm5]], [[1u2d\|1u2d]], [[1u2g\|1u2g]], [[1u28\|1u28]], [[1xlt\|1xlt]], [[2frd\|2frd]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [https://pdbe.org/2fr8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [https://www.ebi.ac.uk/pdbsum/2fr8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fr8 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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [https://pdbe.org/2fr8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [https://www.ebi.ac.uk/pdbsum/2fr8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fr8 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]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dicrospirillum rubrum enderlein 1925]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Boxel, G I.van~~]]	+	[[Category: Rhodospirillum rubrum]]
-	[[Category: Brondijk~~, T H~~]]	+	[[Category: Brondijk TH]]
-	[[Category: Jackson~~, J B~~]]	+	[[Category: Jackson JB]]
-	[[Category: Mather~~, O C~~]]	+	[[Category: Mather OC]]
-	[[Category: Quirk~~, P G~~]]	+	[[Category: Quirk PG]]
-	[[Category: White~~, S A~~]]	+	[[Category: White SA]]
-	[[Category: ~~Nad+]]~~	+	[[Category: Van Boxel GI]]
-	~~[[Category: Nadp+]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 15:32, 3 March 2021

OCA — Wed, 03 Mar 2021 15:32:16 GMT

←Older revision		Revision as of 15:32, 3 March 2021
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	==Structure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymmetric complex==		==Structure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymmetric complex==
-	<StructureSection load='2fr8' size='340' side='right' caption='[[2fr8]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='2fr8' size='340' side='right'caption='[[2fr8]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fr8]] 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=2FR8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2FR8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fr8]] 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=2FR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FR8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hzz\|1hzz]], [[1nm5\|1nm5]], [[1u2d\|1u2d]], [[1u2g\|1u2g]], [[1u28\|1u28]], [[1xlt\|1xlt]], [[2frd\|2frd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1hzz\|1hzz]], [[1nm5\|1nm5]], [[1u2d\|1u2d]], [[1u2g\|1u2g]], [[1u28\|1u28]], [[1xlt\|1xlt]], [[2frd\|2frd]]</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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [~~http~~://pdbe.org/2fr8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2fr8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2fr8 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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [https://pdbe.org/2fr8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [https://www.ebi.ac.uk/pdbsum/2fr8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fr8 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: Boxel, G I.van]]		[[Category: Boxel, G I.van]]
	[[Category: Brondijk, T H]]		[[Category: Brondijk, T H]]

OCA at 06:52, 20 June 2018

OCA — Wed, 20 Jun 2018 06:52:14 GMT

←Older revision		Revision as of 06:52, 20 June 2018
Line 1:		Line 1:
		+
	==Structure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymmetric complex==		==Structure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymmetric complex==
	<StructureSection load='2fr8' size='340' side='right' caption='[[2fr8]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2fr8' size='340' side='right' caption='[[2fr8]], [[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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [http://pdbe.org/2fr8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [http://www.ebi.ac.uk/pdbsum/2fr8 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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [http://pdbe.org/2fr8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [http://www.ebi.ac.uk/pdbsum/2fr8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fr8 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/fr/2fr8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fr/2fr8_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 16:20, 8 February 2016

OCA — Mon, 08 Feb 2016 16:20:18 GMT

←Older revision		Revision as of 16:20, 8 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=2fr8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:20, 10 September 2015

OCA — Thu, 10 Sep 2015 13:20:12 GMT

←Older revision		Revision as of 13:20, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2fr8' size='340' side='right' caption='[[2fr8]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2fr8' size='340' side='right' caption='[[2fr8]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fr8]] 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=2FR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FR8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fr8]] 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=2FR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FR8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hzz\|1hzz]], [[1nm5\|1nm5]], [[1u2d\|1u2d]], [[1u2g\|1u2g]], [[1u28\|1u28]], [[1xlt\|1xlt]], [[2frd\|2frd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hzz\|1hzz]], [[1nm5\|1nm5]], [[1u2d\|1u2d]], [[1u2g\|1u2g]], [[1u28\|1u28]], [[1xlt\|1xlt]], [[2frd\|2frd]]</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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [http://www.ebi.ac.uk/pdbsum/2fr8 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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [http://pdbe.org/2fr8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [http://www.ebi.ac.uk/pdbsum/2fr8 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 2fr8" 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: Boxel, G I.van]]		[[Category: Boxel, G I.van]]
	[[Category: Brondijk, T H]]		[[Category: Brondijk, T H]]

OCA at 00:36, 25 December 2014

OCA — Thu, 25 Dec 2014 00:36:16 GMT

←Older revision		Revision as of 00:36, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fr8]] 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=2FR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FR8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fr8]] 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=2FR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FR8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hzz\|1hzz]], [[1nm5\|1nm5]], [[1u2d\|1u2d]], [[1u2g\|1u2g]], [[1u28\|1u28]], [[1xlt\|1xlt]], [[2frd\|2frd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hzz\|1hzz]], [[1nm5\|1nm5]], [[1u2d\|1u2d]], [[1u2g\|1u2g]], [[1u28\|1u28]], [[1xlt\|1xlt]], [[2frd\|2frd]]</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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [http://www.ebi.ac.uk/pdbsum/2fr8 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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [http://www.ebi.ac.uk/pdbsum/2fr8 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: Boxel, G I.van.]]	+	[[Category: Boxel, G I.van]]
-	[[Category: Brondijk, T H.]]	+	[[Category: Brondijk, T H]]
-	[[Category: Jackson, J B.]]	+	[[Category: Jackson, J B]]
-	[[Category: Mather, O C.]]	+	[[Category: Mather, O C]]
-	[[Category: Quirk, P G.]]	+	[[Category: Quirk, P G]]
-	[[Category: White, S A.]]	+	[[Category: White, S A]]
	[[Category: Nad+]]		[[Category: Nad+]]
	[[Category: Nadp+]]		[[Category: Nadp+]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 07:49, 30 September 2014

OCA — Tue, 30 Sep 2014 07:49:32 GMT

←Older revision		Revision as of 07:49, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2fr8.~~png~~\|~~left~~\|200px]]	+	==Structure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymmetric complex==
		+	<StructureSection load='2fr8' size='340' side='right' caption='[[2fr8]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2fr8]] 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=2FR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FR8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hzz\|1hzz]], [[1nm5\|1nm5]], [[1u2d\|1u2d]], [[1u2g\|1u2g]], [[1u28\|1u28]], [[1xlt\|1xlt]], [[2frd\|2frd]]</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=2fr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fr8 RCSB], [http://www.ebi.ac.uk/pdbsum/2fr8 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/fr/2fr8_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 proton translocation across a membrane to hydride transfer between NADH and NADP+. Previous x-ray structures of complexes of the nucleotide-binding components of transhydrogenase ("dI2dIII1" complexes) indicate that the dihydronicotinamide ring of NADH can move from a distal position relative to the nicotinamide ring of NADP+ to a proximal position. The movement might be responsible for gating hydride transfer during proton translocation. We have mutated three invariant amino acids, Arg-127, Asp-135, and Ser-138, in the NAD(H)-binding site of Rhodospirillum rubrum transhydrogenase. In each mutant, turnover by the intact enzyme is strongly inhibited. Stopped-flow experiments using dI2dIII1 complexes show that inhibition results from a block in the steps associated with hydride transfer. Mutation of Asp-135 and Ser-138 had no effect on the binding affinity of either NAD+ or NADH, but mutation of Arg-127 led to much weaker binding of NADH and slightly weaker binding of NAD+. X-ray structures of dI2dIII1 complexes carrying the mutations showed that their effects were restricted to the locality of the bound NAD(H). The results are consistent with the suggestion that in wild-type protein movement of the Arg-127 side chain, and its hydrogen bonding to Asp-135 and Ser-138, stabilizes the dihydronicotinamide of NADH in the proximal position for hydride transfer.

-	~~{{STRUCTURE_2fr8\| PDB=2fr8 \| SCENE= }}~~	+	The role of invariant amino acid residues at the hydride transfer site of proton-translocating transhydrogenase.,Brondijk TH, van Boxel GI, Mather OC, Quirk PG, White SA, Jackson JB J Biol Chem. 2006 May 12;281(19):13345-54. Epub 2006 Mar 13. PMID:16533815<ref>PMID:16533815</ref>

-	~~===Structure~~ of ~~transhydrogenase (dI~~.~~R127A~~.~~NAD+)2(dIII~~.~~NADP+)1 asymmetric complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_16533815}}~~	+	==See Also==
-		+	*[[NAD(P) transhydrogenase\|NAD(P) transhydrogenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2fr8~~]] 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=2FR8 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:016533815<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
	[[Category: Boxel, G I.van.]]		[[Category: Boxel, G I.van.]]

OCA: Protected "2fr8" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 12:57:47 GMT

Protected "2fr8" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:57, 7 January 2013

OCA at 12:57, 7 January 2013

OCA — Mon, 07 Jan 2013 12:57:42 GMT

←Older revision		Revision as of 12:57, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2fr8.png\|left\|200px]]		[[Image:2fr8.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2fr8", 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_2fr8\| PDB=2fr8 \| SCENE= }}		{{STRUCTURE_2fr8\| PDB=2fr8 \| SCENE= }}

	===Structure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymmetric complex===		===Structure of transhydrogenase (dI.R127A.NAD+)2(dIII.NADP+)1 asymmetric complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16533815}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16533815 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16533815}}		{{ABSTRACT_PUBMED_16533815}}

	==About this Structure==		==About this Structure==
-	~~2FR8~~ 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=2FR8 OCA].	+	[[2fr8]] 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=2FR8 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16533815~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016533815</ref><references group="xtra"/>
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
	[[Category: Boxel, G I.van.]]		[[Category: Boxel, G I.van.]]
Line 34:		Line 22:
	[[Category: Nadp+]]		[[Category: Nadp+]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:23:53 2009''

OCA at 22:23, 16 February 2009

OCA — Mon, 16 Feb 2009 22:23:54 GMT

←Older revision		Revision as of 22:23, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2FR8 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=2FR8 OCA].	+	2FR8 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=2FR8 OCA].

	==Reference==		==Reference==
-	The role of invariant amino acid residues at the hydride transfer site of proton-translocating transhydrogenase., Brondijk TH, van Boxel GI, Mather OC, Quirk PG, White SA, Jackson JB, J Biol Chem. 2006 May 12;281(19):13345-54. Epub 2006 Mar 13. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16533815 16533815]~~	+	<ref group="xtra">PMID:16533815</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Rhodospirillum rubrum]]		[[Category: Rhodospirillum rubrum]]
	[[Category: Boxel, G I.van.]]		[[Category: Boxel, G I.van.]]
Line 36:		Line 35:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 04~~:48:~~02 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:23:53 2009''