1s59: Difference between revisions

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-[[Image:1s59.gif|left|200px]]<br /><applet load="1s59" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1s59, resolution 2.60&Aring;" />
-'''Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis'''<br />
-==Overview==
+==Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis==
-In plants, nucleoside diphosphate kinases (NDPKs) play a key role in the, signaling of both stress and light. However, little is known about the, structural elements involved in their function. Of the three NDPKs, (NDPK1-NDPK3) expressed in Arabidopsis thaliana, NDPK2 is involved in, phytochrome-mediated signal transduction. In this study, we found that the, binding of dNDP or NTP to NDPK2 strengthens the interaction significantly, between activated phytochrome and NDPK2. To better understand the, structural basis of the phytochrome-NDPK2 interaction, we determined the, X-ray structures of NDPK1, NDPK2, and dGTP-bound NDPK2 from A.thaliana at, 1.8A, 2.6A, and 2.4A, respectively. The structures showed that nucleotide, binding caused a slight conformational change in NDPK2 that was confined, to helices alphaA and alpha2. This suggests that the presence of, nucleotide in the active site and/or the evoked conformational change, contributes to the recognition of NDPK2 by activated phytochrome. In vitro, binding assays showed that only NDPK2 interacted specifically with the, phytochrome and the C-terminal regulatory domain of phytochrome is, involved in the interaction. A domain swap experiment between NDPK1 and, NDPK2 showed that the variable C-terminal region of NDPK2 is important for, the activation by phytochrome. The structure of Arabidopsis NDPK1 and, NDPK2 showed that the isoforms share common electrostatic surfaces at the, nucleotide-binding site, but the variable C-terminal regions have distinct, electrostatic charge distributions. These findings suggest that the, binding of nucleotide to NDPK2 plays a regulatory role in phytochrome, signaling and that the C-terminal extension of NDPK2 provides a potential, binding surface for the specific interaction with phytochromes.
+<StructureSection load='1s59' size='340' side='right'caption='[[1s59]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1s59]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S59 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGI:2-DEOXYGUANOSINE-5-DIPHOSPHATE'>DGI</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></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=1s59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s59 OCA], [https://pdbe.org/1s59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s59 RCSB], [https://www.ebi.ac.uk/pdbsum/1s59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s59 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDK2_ARATH NDK2_ARATH] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. May activate MPK3 and MPK6. May be involved in the regulation of cellular redox state and hydrogen peroxide-mediated MAP kinase signaling.<ref>PMID:12506203</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/s5/1s59_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=1s59 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In plants, nucleoside diphosphate kinases (NDPKs) play a key role in the signaling of both stress and light. However, little is known about the structural elements involved in their function. Of the three NDPKs (NDPK1-NDPK3) expressed in Arabidopsis thaliana, NDPK2 is involved in phytochrome-mediated signal transduction. In this study, we found that the binding of dNDP or NTP to NDPK2 strengthens the interaction significantly between activated phytochrome and NDPK2. To better understand the structural basis of the phytochrome-NDPK2 interaction, we determined the X-ray structures of NDPK1, NDPK2, and dGTP-bound NDPK2 from A.thaliana at 1.8A, 2.6A, and 2.4A, respectively. The structures showed that nucleotide binding caused a slight conformational change in NDPK2 that was confined to helices alphaA and alpha2. This suggests that the presence of nucleotide in the active site and/or the evoked conformational change contributes to the recognition of NDPK2 by activated phytochrome. In vitro binding assays showed that only NDPK2 interacted specifically with the phytochrome and the C-terminal regulatory domain of phytochrome is involved in the interaction. A domain swap experiment between NDPK1 and NDPK2 showed that the variable C-terminal region of NDPK2 is important for the activation by phytochrome. The structure of Arabidopsis NDPK1 and NDPK2 showed that the isoforms share common electrostatic surfaces at the nucleotide-binding site, but the variable C-terminal regions have distinct electrostatic charge distributions. These findings suggest that the binding of nucleotide to NDPK2 plays a regulatory role in phytochrome signaling and that the C-terminal extension of NDPK2 provides a potential binding surface for the specific interaction with phytochromes.
-==About this Structure==
+Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling.,Im YJ, Kim JI, Shen Y, Na Y, Han YJ, Kim SH, Song PS, Eom SH J Mol Biol. 2004 Oct 22;343(3):659-70. PMID:15465053<ref>PMID:15465053</ref>
-S59 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with DGI and DGT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S59 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling., Im YJ, Kim JI, Shen Y, Na Y, Han YJ, Kim SH, Song PS, Eom SH, J Mol Biol. 2004 Oct 22;343(3):659-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15465053 15465053]
+</div>
+<div class="pdbe-citations 1s59" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Eom SH]]
-[[Category: Eom, S.H.]]
+[[Category: Han Y-J]]
-[[Category: Han, Y.J.]]
+[[Category: Im YJ]]
-[[Category: Im, Y.J.]]
+[[Category: Kim J-I]]
-[[Category: Kim, J.I.]]
+[[Category: Kim S-H]]
-[[Category: Kim, S.H.]]
+[[Category: Na Y]]
-[[Category: Na, Y.]]
+[[Category: Shen Y]]
-[[Category: Shen, Y.]]
+[[Category: Song P-S]]
-[[Category: Song, P.S.]]
-[[Category: DGI]]
-[[Category: DGT]]
-[[Category: kinase]]
-[[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:06:53 2007''