1z0z - Revision history

OCA at 09:01, 14 February 2024

OCA — Wed, 14 Feb 2024 09:01:55 GMT

←Older revision		Revision as of 09:01, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1z0z' size='340' side='right'caption='[[1z0z]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='1z0z' size='340' side='right'caption='[[1z0z]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1z0z]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arcfl Arcfl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Z0Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1z0z]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z0Z 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>~~</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]] 2.85Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~2234 ARCFL])</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></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'>[https://proteopedia.org/fgij/fg.htm?mol=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [https://pdbe.org/1z0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [https://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z0z ProSAT], [https://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [~~http~~://pdbe.org/1z0z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1z0z ProSAT], [~~http~~://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NADK_ARCFU NADK_ARCFU]] Involved in the regulation of the intracellular balance between NAD(H) and NADP(H), 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:16242716</ref>	+	[https://www.uniprot.org/uniprot/NADK_ARCFU NADK_ARCFU] Involved in the regulation of the intracellular balance between NAD(H) and NADP(H), 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:16242716</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		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/main_output.php?pdb_ID=1z0z 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=1z0z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	NAD kinase is a ubiquitous enzyme that catalyzes the phosphorylation of NAD to NADP using ATP or inorganic polyphosphate (poly(P)) as phosphate donor, and is regarded as the only enzyme responsible for the synthesis of NADP. We present here the crystal structures of an NAD kinase from the archaeal organism Archaeoglobus fulgidus in complex with its phosphate donor ATP at 1.7 A resolution, with its substrate NAD at 3.05 A resolution, and with the product NADP in two different crystal forms at 2.45 A and 2.0 A resolution, respectively. In the ATP bound structure, the AMP portion of the ATP molecule is found to use the same binding site as the nicotinamide ribose portion of NAD/NADP in the NAD/NADP bound structures. A magnesium ion is found to be coordinated to the phosphate tail of ATP as well as to a pyrophosphate group. The conserved GGDG loop forms hydrogen bonds with the pyrophosphate group in the ATP-bound structure and the 2' phosphate group of the NADP in the NADP-bound structures. A possible phosphate transfer mechanism is proposed on the basis of the structures presented.
-
-	Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP.,Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH J Mol Biol. 2005 Nov 25;354(2):289-303. Epub 2005 Sep 30. PMID:16242716<ref>PMID:16242716</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1z0z" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arcfl~~]]	+	[[Category: Archaeoglobus fulgidus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adams~~, P D]]~~	+	[[Category: Adams PD]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Kim R]]
-	[[Category: Kim, R]]	+	[[Category: Kim SH]]
-	[[Category: Kim~~, S H~~]]	+	[[Category: Liu J]]
-	[[Category: Liu, J]]	+	[[Category: Lou Y]]
-	[[Category: Lou, Y]]	+	[[Category: Yokota H]]
-	[[Category: Yokota, H]]	+
-	~~[[Category: Atp]]~~	+
-	~~[[Category: Bsgc]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Nad kinase]]~~	+
-	~~[[Category: Nadp]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:56, 20 January 2021

OCA — Wed, 20 Jan 2021 08:56:41 GMT

←Older revision		Revision as of 08:56, 20 January 2021
Line 1:		Line 1:

	==Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD==		==Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD==
-	<StructureSection load='1z0z' size='340' side='right' caption='[[1z0z]], [[Resolution\|resolution]] 2.85Å' scene=''>	+	<StructureSection load='1z0z' size='340' side='right'caption='[[1z0z]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1z0z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Z0Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1z0z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Z0Z 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></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></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [http://pdbe.org/1z0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [http://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z0z ProSAT], [http://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [http://pdbe.org/1z0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [http://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z0z ProSAT], [http://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Arcfl]]		[[Category: Arcfl]]
		+	[[Category: Large Structures]]
	[[Category: Adams, P D]]		[[Category: Adams, P D]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 07:06, 25 April 2018

OCA — Wed, 25 Apr 2018 07:06:38 GMT

←Older revision		Revision as of 07:06, 25 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD==		==Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD==
	<StructureSection load='1z0z' size='340' side='right' caption='[[1z0z]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='1z0z' size='340' side='right' caption='[[1z0z]], [[Resolution\|resolution]] 2.85Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [http://pdbe.org/1z0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [http://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [http://pdbe.org/1z0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [http://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z0z ProSAT], [http://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z0/1z0z_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z0/1z0z_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>
	</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=1z0z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1z0z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1z0z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[NAD kinase\|NAD kinase]]
	== References ==		== References ==
	<references/>		<references/>
Line 41:		Line 45:
	[[Category: Lou, Y]]		[[Category: Lou, Y]]
	[[Category: Yokota, H]]		[[Category: Yokota, H]]
		+	[[Category: Atp]]
	[[Category: Bsgc]]		[[Category: Bsgc]]
	[[Category: Nad]]		[[Category: Nad]]

OCA at 13:24, 11 September 2015

OCA — Fri, 11 Sep 2015 13:24:50 GMT

←Older revision		Revision as of 13:24, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1z0z' size='340' side='right' caption='[[1z0z]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='1z0z' size='340' side='right' caption='[[1z0z]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1z0z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Archaeoglobus_fulgidus Archaeoglobus fulgidus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z0Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1z0z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z0Z 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></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></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ~~Archaeoglobus fulgidus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [http://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [http://pdbe.org/1z0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [http://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~PPNK_ARCFU PPNK_ARCFU~~]] Involved in the regulation of the intracellular balance between NAD(H) and NADP(H), 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:16242716</ref>	+	[[http://www.uniprot.org/uniprot/NADK_ARCFU NADK_ARCFU]] Involved in the regulation of the intracellular balance between NAD(H) and NADP(H), 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:16242716</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	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 1z0z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Archaeoglobus fulgidus~~]]	+	[[Category: Arcfl]]
	[[Category: Adams, P D]]		[[Category: Adams, P D]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 17:01, 25 December 2014

OCA — Thu, 25 Dec 2014 17:01:33 GMT

←Older revision		Revision as of 17:01, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1z0z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z0Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[1z0z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z0Z 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><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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [http://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [http://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PPNK_ARCFU PPNK_ARCFU]] Involved in the regulation of the intracellular balance between NAD(H) and NADP(H), 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:16242716</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
-	[[Category: Adams, P D.]]	+	[[Category: Adams, P D]]
-	[[Category: ~~BSGC, Berkeley~~ Structural ~~Genomics Center.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Kim, R.]]	+	[[Category: Kim, R]]
-	[[Category: Kim, S H.]]	+	[[Category: Kim, S H]]
-	[[Category: Liu, J.]]	+	[[Category: Liu, J]]
-	[[Category: Lou, Y.]]	+	[[Category: Lou, Y]]
-	[[Category: Yokota, H~~.]]~~	+	[[Category: Yokota, H]]
-	~~[[Category: Berkeley structural genomics center~~]]	+
	[[Category: Bsgc]]		[[Category: Bsgc]]
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Nad kinase]]		[[Category: Nad kinase]]
	[[Category: Nadp]]		[[Category: Nadp]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi]]~~	+
-	~~[[Category: Structural genomic~~]]	+
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 20:14, 29 September 2014

OCA — Mon, 29 Sep 2014 20:14:48 GMT

←Older revision		Revision as of 20:14, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1z0z.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD==
		+	<StructureSection load='1z0z' size='340' side='right' caption='[[1z0z]], [[Resolution\|resolution]] 2.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1z0z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z0Z 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><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</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=1z0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB], [http://www.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://www.topsan.org/Proteins/BSGC/1z0z TOPSAN]</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/z0/1z0z_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 ==
		+	NAD kinase is a ubiquitous enzyme that catalyzes the phosphorylation of NAD to NADP using ATP or inorganic polyphosphate (poly(P)) as phosphate donor, and is regarded as the only enzyme responsible for the synthesis of NADP. We present here the crystal structures of an NAD kinase from the archaeal organism Archaeoglobus fulgidus in complex with its phosphate donor ATP at 1.7 A resolution, with its substrate NAD at 3.05 A resolution, and with the product NADP in two different crystal forms at 2.45 A and 2.0 A resolution, respectively. In the ATP bound structure, the AMP portion of the ATP molecule is found to use the same binding site as the nicotinamide ribose portion of NAD/NADP in the NAD/NADP bound structures. A magnesium ion is found to be coordinated to the phosphate tail of ATP as well as to a pyrophosphate group. The conserved GGDG loop forms hydrogen bonds with the pyrophosphate group in the ATP-bound structure and the 2' phosphate group of the NADP in the NADP-bound structures. A possible phosphate transfer mechanism is proposed on the basis of the structures presented.

-	~~{{STRUCTURE_1z0z\| PDB=1z0z \| SCENE= }}~~	+	Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP.,Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH J Mol Biol. 2005 Nov 25;354(2):289-303. Epub 2005 Sep 30. PMID:16242716<ref>PMID:16242716</ref>

-	~~===Crystal structure~~ of ~~a NAD kinase from Archaeoglobus fulgidus in complex with NAD===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16242716}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1z0z]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016242716<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Adams, P D.]]		[[Category: Adams, P D.]]

OCA: Protected "1z0z" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 17:52:05 GMT

Protected "1z0z" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:52, 5 January 2013

OCA at 17:52, 5 January 2013

OCA — Sat, 05 Jan 2013 17:52:03 GMT

←Older revision		Revision as of 17:52, 5 January 2013
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-	{{Seed}}
	[[Image:1z0z.png\|left\|200px]]		[[Image:1z0z.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1z0z", 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_1z0z\| PDB=1z0z \| SCENE= }}		{{STRUCTURE_1z0z\| PDB=1z0z \| SCENE= }}

	===Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD===		===Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16242716}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16242716 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16242716}}		{{ABSTRACT_PUBMED_16242716}}

	==About this Structure==		==About this Structure==
-	~~1Z0Z~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA].	+	[[1z0z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16242716~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016242716</ref><references group="xtra"/>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Adams, P D.]]		[[Category: Adams, P D.]]
Line 32:		Line 20:
	[[Category: Lou, Y.]]		[[Category: Lou, Y.]]
	[[Category: Yokota, H.]]		[[Category: Yokota, H.]]
-	[[Category: Atp]]
	[[Category: Berkeley structural genomics center]]		[[Category: Berkeley structural genomics center]]
	[[Category: Bsgc]]		[[Category: Bsgc]]
Line 41:		Line 28:
	[[Category: Psi]]		[[Category: Psi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 22:44:57 2009''~~	+

OCA at 20:45, 17 February 2009

OCA — Tue, 17 Feb 2009 20:45:12 GMT

←Older revision		Revision as of 20:45, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP., Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH, J Mol Biol. 2005 Nov 25;354(2):289-303. Epub 2005 Sep 30. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16242716 16242716]~~	+	<ref group="xtra">PMID:16242716</ref><references group="xtra"/>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Adams, P D.]]		[[Category: Adams, P D.]]
Line 42:		Line 42:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 14~~:42:~~53 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:44:57 2009''

OCA at 12:42, 16 November 2008

OCA — Sun, 16 Nov 2008 12:42:55 GMT

←Older revision		Revision as of 12:42, 16 November 2008
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1Z0Z is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA].	+	1Z0Z is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0Z OCA].

	==Reference==		==Reference==
	Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP., Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH, J Mol Biol. 2005 Nov 25;354(2):289-303. Epub 2005 Sep 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16242716 16242716]		Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP., Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH, J Mol Biol. 2005 Nov 25;354(2):289-303. Epub 2005 Sep 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16242716 16242716]
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
-	[[Category: Single protein]]
	[[Category: Adams, P D.]]		[[Category: Adams, P D.]]
	[[Category: BSGC, Berkeley Structural Genomics Center.]]		[[Category: BSGC, Berkeley Structural Genomics Center.]]
Line 43:		Line 42:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 06~~:48:02 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 14:42:53 2008''