2o7p - Revision history

OCA at 08:23, 30 October 2024

2024-10-30T08:23:00Z

← Older revision		Revision as of 08:23, 30 October 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o7/2o7p_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o7/2o7p_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 08:56, 25 October 2023

2023-10-25T08:56:44Z

← Older revision		Revision as of 08:56, 25 October 2023
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	<StructureSection load='2o7p' size='340' side='right'caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2o7p' size='340' side='right'caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O7P FirstGlance]. <br>		<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O7P 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>~~</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]] 3Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[2g6v\|2g6v]]~~</~~div~~></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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [https://pdbe.org/2o7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [https://www.ebi.ac.uk/pdbsum/2o7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7p 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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [https://pdbe.org/2o7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [https://www.ebi.ac.uk/pdbsum/2o7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/~~RIBD_ECOLI RIBD_ECOLI]~~] Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.		[https://www.uniprot.org/uniprot/Q3ZUB0_ECOLX Q3ZUB0_ECOLX] Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.[ARBA:ARBA00002151][PIRNR:PIRNR006769]
	== 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: ~~Ecoli~~]]		[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gurmu, D]]		[[Category: Gurmu D]]
	[[Category: Moche, M]]		[[Category: Moche M]]
	[[Category: Nordlund, P]]		[[Category: Nordlund P]]
	~~[[Category: SPINE, Structural Proteomics in Europe~~]]		[[Category: Stenmark P]]
	[[Category: Stenmark, P]]
	~~[[Category: Alpha and beta class with mainly parallell beta strand]]~~
	~~[[Category: Htp-protein escherichia coli]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Nadp+ complex]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Spine]]~~
	~~[[Category: Structural genomic]]~~
	~~[[Category: Structural proteomics in europe~~]]

OCA at 07:50, 2 March 2022

2022-03-02T07:50:19Z

← Older revision		Revision as of 07:50, 2 March 2022
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	<StructureSection load='2o7p' size='340' side='right'caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2o7p' size='340' side='right'caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2O7P FirstGlance]. <br>		<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O7P 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2g6v\|2g6v]]</div></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [~~http~~://pdbe.org/2o7p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2o7p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7p 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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [https://pdbe.org/2o7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [https://www.ebi.ac.uk/pdbsum/2o7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/RIBD_ECOLI RIBD_ECOLI]] Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.		[[https://www.uniprot.org/uniprot/RIBD_ECOLI RIBD_ECOLI]] Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:58, 27 May 2020

2020-05-27T07:58:18Z

← Older revision		Revision as of 07:58, 27 May 2020
Line 1:		Line 1:

	==The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain==		==The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain==
	<StructureSection load='2o7p' size='340' side='right' caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2o7p' size='340' side='right'caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2O7P FirstGlance]. <br>		<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2O7P 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [http://pdbe.org/2o7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [http://www.ebi.ac.uk/pdbsum/2o7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7p 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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [http://pdbe.org/2o7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [http://www.ebi.ac.uk/pdbsum/2o7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
			[[Category: Large Structures]]
	[[Category: Gurmu, D]]		[[Category: Gurmu, D]]
	[[Category: Moche, M]]		[[Category: Moche, M]]

OCA at 07:33, 22 August 2018

2018-08-22T07:33:31Z

← Older revision		Revision as of 07:33, 22 August 2018
Line 1:		Line 1:

	==The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain==		==The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain==
	<StructureSection load='2o7p' size='340' side='right' caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2o7p' size='340' side='right' caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [http://pdbe.org/2o7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [http://www.ebi.ac.uk/pdbsum/2o7p 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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [http://pdbe.org/2o7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [http://www.ebi.ac.uk/pdbsum/2o7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o7/2o7p_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o7/2o7p_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 14:03, 8 February 2016

2016-02-08T14:03:38Z

← Older revision		Revision as of 14:03, 8 February 2016
Line 6:		Line 6:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [http://www.ebi.ac.uk/pdbsum/2o7p 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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [http://pdbe.org/2o7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [http://www.ebi.ac.uk/pdbsum/2o7p PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=2o7p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 2o7p" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:59, 3 June 2015

2015-06-03T06:59:25Z

← Older revision		Revision as of 06:59, 3 June 2015
Line 2:		Line 2:
	<StructureSection load='2o7p' size='340' side='right' caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2o7p' size='340' side='right' caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O7P FirstGlance]. <br>		<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O7P 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
Line 20:		Line 20:
	</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/chain_selection.php?pdb_ID=2ata ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			We have determined the crystal structure of the bi-functional deaminase/reductase enzyme from Escherichia coli (EcRibD) that catalyzes two consecutive reactions during riboflavin biosynthesis. The polypeptide chain of EcRibD is folded into two domains where the 3D structure of the N-terminal domain (1-145) is similar to cytosine deaminase and the C-terminal domain (146-367) is similar to dihydrofolate reductase. We showed that EcRibD is dimeric and compared our structure to tetrameric RibG, an ortholog from Bacillus subtilis (BsRibG). We have also determined the structure of EcRibD in two binary complexes with the oxidized cofactor (NADP(+)) and with the substrate analogue ribose-5-phosphate (RP5) and superposed these two in order to mimic the ternary complex. Based on this superposition we propose that the invariant Asp200 initiates the reductive reaction by abstracting a proton from the bound substrate and that the pro-R proton from C4 of the cofactor is transferred to C1 of the substrate. A highly flexible loop is found in the reductase active site (159-173) that appears to control cofactor and substrate binding to the reductase active site and was therefore compared to the corresponding Met20 loop of E. coli dihydrofolate reductase (EcDHFR). Lys152, identified by comparing substrate analogue (RP5) coordination in the reductase active site of EcRibD with the homologous reductase from Methanocaldococcus jannaschii (MjaRED), is invariant among bacterial RibD enzymes and could contribute to the various pathways taken during riboflavin biosynthesis in bacteria and yeast.

			The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism.,Stenmark P, Moche M, Gurmu D, Nordlund P J Mol Biol. 2007 Oct 12;373(1):48-64. Epub 2006 Dec 8. PMID:17765262<ref>PMID:17765262</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia coli k-12~~]]		[[Category: Ecoli]]
	[[Category: Gurmu, D]]		[[Category: Gurmu, D]]
	[[Category: Moche, M]]		[[Category: Moche, M]]

OCA at 23:51, 24 December 2014

2014-12-24T23:51:57Z

← Older revision		Revision as of 23:51, 24 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O7P FirstGlance]. <br>		<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O7P 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><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></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [http://www.ebi.ac.uk/pdbsum/2o7p 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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [http://www.ebi.ac.uk/pdbsum/2o7p PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/RIBD_ECOLI RIBD_ECOLI]] Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Gurmu, D.]]		[[Category: Gurmu, D]]
	[[Category: Moche, M.]]		[[Category: Moche, M]]
	[[Category: Nordlund, P.]]		[[Category: Nordlund, P]]
	[[Category: SPINE, Structural Proteomics in Europe.]]		[[Category: SPINE, Structural Proteomics in Europe]]
	[[Category: Stenmark, P.]]		[[Category: Stenmark, P]]
	[[Category: Alpha and beta class with mainly parallell beta strand]]		[[Category: Alpha and beta class with mainly parallell beta strand]]
	[[Category: Htp-protein escherichia coli]]		[[Category: Htp-protein escherichia coli]]

OCA at 19:44, 30 September 2014

2014-09-30T19:44:24Z

← Older revision		Revision as of 19:44, 30 September 2014
Line 1:		Line 1:
	~~[[Image:2o7p.png\|left\|200px]]~~		==The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain==
			<StructureSection load='2o7p' size='340' side='right' caption='[[2o7p]], [[Resolution\|resolution]] 3.00Å' scene=''>
	~~{{STRUCTURE_2o7p\| PDB=2o7p \| SCENE= }}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2o7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O7P FirstGlance]. <br>
	===The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain===		</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><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	~~{{ABSTRACT_PUBMED_017765262}}~~		<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</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=2o7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o7p RCSB], [http://www.ebi.ac.uk/pdbsum/2o7p PDBsum]</span></td></tr>
	==~~About this Structure~~==		<table>
	[[2o7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7P OCA].		== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
	==~~Reference~~==		Check<jmol>
	<~~ref group~~="~~xtra~~">~~PMID~~:~~017765262~~</~~ref~~><~~references group~~="~~xtra~~"/>		<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o7/2o7p_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>
			__TOC__
			</StructureSection>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Gurmu, D.]]		[[Category: Gurmu, D.]]

OCA: Protected "2o7p" [edit=sysop:move=sysop]

2013-01-07T12:08:05Z

Protected "2o7p" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:08, 7 January 2013
(No difference)