2i2c: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:2i2c.jpg|left|200px]]<br /><applet load="2i2c" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2i2c, resolution 1.850&Aring;" />
-'''Crystal structure of LmNADK1'''<br />
-==About this Structure==
+==Crystal structure of LmNADK1==
-I2C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Listeria_monocytogenes Listeria monocytogenes] with <scene name='pdbligand=DTA:'>DTA</scene> and <scene name='pdbligand=PG4:'>PG4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2C OCA].
+<StructureSection load='2i2c' size='340' side='right'caption='[[2i2c]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-[[Category: Listeria monocytogenes]]
+== Structural highlights ==
-[[Category: NAD(+) kinase]]
+<table><tr><td colspan='2'>[[2i2c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes_EGD-e Listeria monocytogenes EGD-e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I2C FirstGlance]. <br>
-[[Category: Single protein]]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
-[[Category: G., Labesse.]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTA:(2S,3S,4R,5R,2S,3S,4R,5R)-2,2-[DITHIOBIS(METHYLENE)]BIS[5-(6-AMINO-9H-PURIN-9-YL)TETRAHYDROFURAN-3,4-DIOL]'>DTA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-[[Category: G., Poncet-Montange.]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2i2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2c OCA], [https://pdbe.org/2i2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i2c RCSB], [https://www.ebi.ac.uk/pdbsum/2i2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i2c ProSAT]</span></td></tr>
-[[Category: DTA]]
+</table>
-[[Category: PG4]]
+== Function ==
-[[Category: nadp bound crystal structure of lmnadk1]]
+[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>
-[[Category: transferase]]
+== 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/i2/2i2c_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=2i2c 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.
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:15:58 2008''
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2i2c" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[NAD kinase|NAD kinase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Listeria monocytogenes EGD-e]]
+[[Category: Labesse G]]
+[[Category: Poncet-Montange G]]