2i2f - Revision history

OCA at 10:05, 30 August 2023

2023-08-30T10:05:21Z

← Older revision		Revision as of 10:05, 30 August 2023
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	<StructureSection load='2i2f' size='340' side='right'caption='[[2i2f]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2i2f' size='340' side='right'caption='[[2i2f]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2i2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium~~ monocytogenes ~~hominis" nyfeldt 1932~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I2F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2i2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I2F FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE~~-~~DINUCLEOTIDE'>NAD</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em~~;~~'>[[2i1w\|2i1w]], [[2i29\|2i29]], [[2i2a\|2i2a]], [[2i2b\|2i2b]], [[2i2c\|2i2c]], [[2i2d\|2i2d]], [[2i2e\|2i2e]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ppnK1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1639~~ "~~Bacterium monocytogenes hominis~~" ~~Nyfeldt 1932])~~<~~/td~~></tr>
	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23]~~ </~~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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [https://pdbe.org/2i2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [https://www.ebi.ac.uk/pdbsum/2i2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i2f 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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [https://pdbe.org/2i2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [https://www.ebi.ac.uk/pdbsum/2i2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i2f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>		[https://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>
	== 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: Bacterium monocytogenes hominis nyfeldt 1932]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Arold, S]]		[[Category: Listeria monocytogenes]]
	[[Category: Assairi, L]]		[[Category: Arold S]]
	[[Category: Labesse, G]]		[[Category: Assairi L]]
	[[Category: Pochet, S]]		[[Category: Labesse G]]
	[[Category: Poncet-Montange, G]]		[[Category: Pochet S]]
	~~[[Category: Crystal structure of lmnadk1 bound to a nad analog]]~~		[[Category: Poncet-Montange G]]
	~~[[Category: Transferase~~]]

OCA at 07:26, 24 March 2021

2021-03-24T07:26:38Z

← Older revision		Revision as of 07:26, 24 March 2021
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	==Crystal structure of LmNADK1==		==Crystal structure of LmNADK1==
	<StructureSection load='2i2f' size='340' side='right' caption='[[2i2f]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2i2f' size='340' side='right'caption='[[2i2f]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2i2f]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2I2F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2i2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I2F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i1w\|2i1w]], [[2i29\|2i29]], [[2i2a\|2i2a]], [[2i2b\|2i2b]], [[2i2c\|2i2c]], [[2i2d\|2i2d]], [[2i2e\|2i2e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2i1w\|2i1w]], [[2i29\|2i29]], [[2i2a\|2i2a]], [[2i2b\|2i2b]], [[2i2c\|2i2c]], [[2i2d\|2i2d]], [[2i2e\|2i2e]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 "Bacterium monocytogenes hominis" Nyfeldt 1932])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 "Bacterium monocytogenes hominis" Nyfeldt 1932])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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(+)_kinase NAD(+) kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [~~http~~://pdbe.org/2i2f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2i2f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2i2f 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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [https://pdbe.org/2i2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [https://www.ebi.ac.uk/pdbsum/2i2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i2f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>		[[https://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 2i2f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2i2f" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[NAD kinase\|NAD kinase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacterium monocytogenes hominis nyfeldt 1932]]		[[Category: Bacterium monocytogenes hominis nyfeldt 1932]]
			[[Category: Large Structures]]
	[[Category: Arold, S]]		[[Category: Arold, S]]
	[[Category: Assairi, L]]		[[Category: Assairi, L]]

OCA at 06:46, 15 February 2018

2018-02-15T06:46:27Z

← Older revision		Revision as of 06:46, 15 February 2018
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	==Crystal structure of LmNADK1==		==Crystal structure of LmNADK1==
	<StructureSection load='2i2f' size='340' side='right' caption='[[2i2f]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2i2f' size='340' side='right' caption='[[2i2f]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 "Bacterium monocytogenes hominis" Nyfeldt 1932])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 "Bacterium monocytogenes hominis" Nyfeldt 1932])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [http://pdbe.org/2i2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [http://www.ebi.ac.uk/pdbsum/2i2f 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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [http://pdbe.org/2i2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [http://www.ebi.ac.uk/pdbsum/2i2f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2i2f 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/i2/2i2f_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i2/2i2f_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>
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	</div>		</div>
	<div class="pdbe-citations 2i2f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2i2f" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[NAD kinase\|NAD kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:25, 9 February 2016

2016-02-09T13:25:20Z

← Older revision		Revision as of 13:25, 9 February 2016
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	<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=2i2f 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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	</div>		</div>
	<div class="pdbe-citations 2i2f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2i2f" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[NAD kinase\|NAD kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:39, 10 September 2015

2015-09-10T22:39:51Z

← Older revision		Revision as of 22:39, 10 September 2015
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	<StructureSection load='2i2f' size='340' side='right' caption='[[2i2f]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2i2f' size='340' side='right' caption='[[2i2f]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2i2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Listeria_monocytogenes Listeria~~ monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I2F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2i2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I2F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i1w\|2i1w]], [[2i29\|2i29]], [[2i2a\|2i2a]], [[2i2b\|2i2b]], [[2i2c\|2i2c]], [[2i2d\|2i2d]], [[2i2e\|2i2e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i1w\|2i1w]], [[2i29\|2i29]], [[2i2a\|2i2a]], [[2i2b\|2i2b]], [[2i2c\|2i2c]], [[2i2d\|2i2d]], [[2i2e\|2i2e]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 ~~Listeria~~ monocytogenes])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 "Bacterium monocytogenes hominis" Nyfeldt 1932])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [http://www.ebi.ac.uk/pdbsum/2i2f 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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [http://pdbe.org/2i2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [http://www.ebi.ac.uk/pdbsum/2i2f PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/~~PPNK1_LISMO PPNK1_LISMO~~]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>		[[http://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 2i2f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Listeria~~ monocytogenes]]		[[Category: Bacterium monocytogenes hominis nyfeldt 1932]]
	[[Category: Arold, S]]		[[Category: Arold, S]]
	[[Category: Assairi, L]]		[[Category: Assairi, L]]

OCA at 07:05, 25 December 2014

2014-12-25T07:05:03Z

← Older revision		Revision as of 07:05, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2i2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I2F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2i2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I2F FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i1w\|2i1w]], [[2i29\|2i29]], [[2i2a\|2i2a]], [[2i2b\|2i2b]], [[2i2c\|2i2c]], [[2i2d\|2i2d]], [[2i2e\|2i2e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i1w\|2i1w]], [[2i29\|2i29]], [[2i2a\|2i2a]], [[2i2b\|2i2b]], [[2i2c\|2i2c]], [[2i2d\|2i2d]], [[2i2e\|2i2e]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 Listeria monocytogenes])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 Listeria monocytogenes])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [http://www.ebi.ac.uk/pdbsum/2i2f 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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [http://www.ebi.ac.uk/pdbsum/2i2f PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/PPNK1_LISMO PPNK1_LISMO]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>
	== 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: Listeria monocytogenes]]		[[Category: Listeria monocytogenes]]
	[[Category: Arold, S.]]		[[Category: Arold, S]]
	[[Category: Assairi, L.]]		[[Category: Assairi, L]]
	[[Category: Labesse, G.]]		[[Category: Labesse, G]]
	[[Category: Pochet, S.]]		[[Category: Pochet, S]]
	[[Category: Poncet-Montange, G.]]		[[Category: Poncet-Montange, G]]
	[[Category: Crystal structure of lmnadk1 bound to a nad analog]]		[[Category: Crystal structure of lmnadk1 bound to a nad analog]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:01, 30 September 2014

2014-09-30T08:01:47Z

← Older revision		Revision as of 08:01, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2i2f~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of LmNADK1==
			<StructureSection load='2i2f' size='340' side='right' caption='[[2i2f]], [[Resolution\|resolution]] 1.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2i2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I2F FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i1w\|2i1w]], [[2i29\|2i29]], [[2i2a\|2i2a]], [[2i2b\|2i2b]], [[2i2c\|2i2c]], [[2i2d\|2i2d]], [[2i2e\|2i2e]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 Listeria monocytogenes])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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=2i2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i2f RCSB], [http://www.ebi.ac.uk/pdbsum/2i2f 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/i2/2i2f_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 ==
			Here we describe the crystal structures of the NAD kinase (LmNADK1) from Listeria monocytogenes in complex with its substrate NAD, its product NADP, or two synthesized NAD mimics. We identified one of the NAD mimics, di-adenosine diphosphate, as a new substrate for LmNADK1, whereas we showed that the closely related compound di-5'-thioadenosine is a novel non-natural inhibitor for this enzyme. These structures suggest a mechanism involving substrate-assisted catalysis. Indeed, sequence/structure comparison and directed mutagenesis have previously shown that NAD kinases (NADKs) and the distantly related 6-phosphofructokinases share the same catalytically important GGDGT motif. However, in this study we have shown that these enzymes use the central aspartate of this motif differently. Although this acidic residue chelates the catalytic Mg(2+) ion in 6-phosphofructokinases, it activates the phospho-acceptor (NAD) in NADKs. Sequence/structure comparisons suggest that the role of this aspartate would be conserved in NADKs and the related sphingosine and diacylglycerol kinases.

	~~{{STRUCTURE_2i2f\| PDB=2i2f \| SCENE= }}~~		NAD kinases use substrate-assisted catalysis for specific recognition of NAD.,Poncet-Montange G, Assairi L, Arold S, Pochet S, Labesse G J Biol Chem. 2007 Nov 23;282(47):33925-34. Epub 2007 Aug 8. PMID:17686780<ref>PMID:17686780</ref>

	~~===Crystal structure~~ of ~~LmNADK1===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17686780}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2i2f]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Listeria_monocytogenes Listeria monocytogenes]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017686780<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Listeria monocytogenes]]		[[Category: Listeria monocytogenes]]
	[[Category: Arold, S.]]		[[Category: Arold, S.]]

OCA: Protected "2i2f" [edit=sysop:move=sysop]

2013-01-07T18:06:04Z

Protected "2i2f" [edit=sysop:move=sysop]

← Older revision	Revision as of 18:06, 7 January 2013
(No difference)

OCA at 18:06, 7 January 2013

2013-01-07T18:06:02Z

← Older revision		Revision as of 18:06, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2i2f.png\|left\|200px]]		[[Image:2i2f.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2i2f", 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_2i2f\| PDB=2i2f \| SCENE= }}		{{STRUCTURE_2i2f\| PDB=2i2f \| SCENE= }}

	===Crystal structure of LmNADK1===		===Crystal structure of LmNADK1===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17686780}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17686780 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17686780}}		{{ABSTRACT_PUBMED_17686780}}

	==About this Structure==		==About this Structure==
	~~2I2F~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA].		[[2i2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17686780~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017686780</ref><references group="xtra"/>
	[[Category: Listeria monocytogenes]]		[[Category: Listeria monocytogenes]]
	[[Category: Arold, S.]]		[[Category: Arold, S.]]
Line 32:		Line 20:
	[[Category: Crystal structure of lmnadk1 bound to a nad analog]]		[[Category: Crystal structure of lmnadk1 bound to a nad analog]]
	[[Category: Transferase]]		[[Category: Transferase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:06:29 2009''~~

OCA at 08:06, 17 February 2009

2009-02-17T08:06:30Z

← Older revision		Revision as of 08:06, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2I2F is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA].		2I2F is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2F OCA].

	==Reference==		==Reference==
	~~NAD kinases use substrate-assisted catalysis for specific recognition of NAD., Poncet-Montange G, Assairi L, Arold S, Pochet S, Labesse G, J Biol Chem. 2007 Nov 23;282(47):33925-34. Epub 2007 Aug 8.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17686780 17686780]~~		<ref group="xtra">PMID:17686780</ref><references group="xtra"/>
	[[Category: Listeria monocytogenes]]		[[Category: Listeria monocytogenes]]
	~~[[Category: Single protein]]~~
	[[Category: Arold, S.]]		[[Category: Arold, S.]]
	[[Category: Assairi, L.]]		[[Category: Assairi, L.]]
Line 34:		Line 33:
	[[Category: Transferase]]		[[Category: Transferase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Nov 5~~ 10:49:~~00 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:06:29 2009''