1z0z: Difference between revisions

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-[[Image:1z0z.gif|left|200px]]
- {{Structure
+==Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD==
-|PDB= 1z0z |SIZE=350|CAPTION= <scene name='initialview01'>1z0z</scene>, resolution 2.85&Aring;
+<StructureSection load='1z0z' size='340' side='right'caption='[[1z0z]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
+<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>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85&#8491;</td></tr>
-|GENE= ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])
+<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>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG0061 nadF]</span>
+<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>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<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.ebi.ac.uk/pdbsum/1z0z PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1z0z RCSB]</span>
+== Function ==
-}}
+[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 ==
+[[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/main_output.php?pdb_ID=1z0z ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD'''
+==See Also==
+*[[NAD kinase|NAD kinase]]
+== References ==
-==Overview==
+<references/>
-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.
+__TOC__
+</StructureSection>
-==About this Structure==
-Z0Z 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].
-==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]
 [[Category: Archaeoglobus fulgidus]]
-[[Category: NAD(+) kinase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Adams PD]]
-[[Category: Adams, P D.]]
+[[Category: Kim R]]
-[[Category: BSGC, Berkeley Structural Genomics Center.]]
+[[Category: Kim SH]]
-[[Category: Kim, R.]]
+[[Category: Liu J]]
-[[Category: Kim, S H.]]
+[[Category: Lou Y]]
-[[Category: Liu, J.]]
+[[Category: Yokota H]]
-[[Category: Lou, Y.]]
-[[Category: Yokota, H.]]
-[[Category: atp]]
-[[Category: berkeley structural genomics center]]
-[[Category: bsgc]]
-[[Category: nad]]
-[[Category: nad kinase]]
-[[Category: nadp]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:27:26 2008''