1nsp: Difference between revisions

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-[[Image:1nsp.gif|left|200px]]<br /><applet load="1nsp" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1nsp, resolution 2.1&Aring;" />
-'''MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE: X-RAY STRUCTURES OF A PHOSPHO-HISTIDINE INTERMEDIATE OF THE ENZYMES FROM DROSOPHILA AND DICTYOSTELIUM'''<br />
-==Overview==
+==MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE: X-RAY STRUCTURES OF A PHOSPHO-HISTIDINE INTERMEDIATE OF THE ENZYMES FROM DROSOPHILA AND DICTYOSTELIUM==
-Nucleoside diphosphate kinase (NDP kinase) has a ping-pong mechanism with, a phosphohistidine intermediate. Crystals of the enzymes from, Dictyostelium discoideum and from Drosophila melanogaster were treated, with phosphoramidate, and their X-ray structures were determined at 2.1, and 2.2 A resolution, respectively. The atomic models, refined to R, factors below 20%, show no conformation change relative to the free, proteins. In both enzymes, the active site histidine was phosphorylated on, N delta, and it was the only site of phosphorylation. The phosphate group, interacts with the hydroxyl group of Tyr56 and with protein-bound water, molecules. Its environment is compared with that of phosphohistidines in, succinyl-CoA synthetase and in phosphocarrier proteins. The X-ray, structures of phosphorylated NDP kinase and of previously determined, complexes with nucleoside diphosphates provide a basis for modeling the, Michaelis complex with a nucleoside triphosphate, that of the, phosphorylated protein with a nucleoside diphosphate, and the transition, state of the phosphate transfer reaction in which the gamma-phosphate is, pentacoordinated.
+<StructureSection load='1nsp' size='340' side='right'caption='[[1nsp]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1nsp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NSP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NSP 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]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HIP:ND1-PHOSPHONOHISTIDINE'>HIP</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=1nsp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nsp OCA], [https://pdbe.org/1nsp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nsp RCSB], [https://www.ebi.ac.uk/pdbsum/1nsp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nsp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
+== 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/ns/1nsp_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=1nsp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nucleoside diphosphate kinase (NDP kinase) has a ping-pong mechanism with a phosphohistidine intermediate. Crystals of the enzymes from Dictyostelium discoideum and from Drosophila melanogaster were treated with phosphoramidate, and their X-ray structures were determined at 2.1 and 2.2 A resolution, respectively. The atomic models, refined to R factors below 20%, show no conformation change relative to the free proteins. In both enzymes, the active site histidine was phosphorylated on N delta, and it was the only site of phosphorylation. The phosphate group interacts with the hydroxyl group of Tyr56 and with protein-bound water molecules. Its environment is compared with that of phosphohistidines in succinyl-CoA synthetase and in phosphocarrier proteins. The X-ray structures of phosphorylated NDP kinase and of previously determined complexes with nucleoside diphosphates provide a basis for modeling the Michaelis complex with a nucleoside triphosphate, that of the phosphorylated protein with a nucleoside diphosphate, and the transition state of the phosphate transfer reaction in which the gamma-phosphate is pentacoordinated.
-==About this Structure==
+Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium.,Morera S, Chiadmi M, LeBras G, Lascu I, Janin J Biochemistry. 1995 Sep 5;34(35):11062-70. PMID:7669763<ref>PMID:7669763</ref>
-NSP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. 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=1NSP OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium., Morera S, Chiadmi M, LeBras G, Lascu I, Janin J, Biochemistry. 1995 Sep 5;34(35):11062-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7669763 7669763]
+</div>
+<div class="pdbe-citations 1nsp" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Dictyostelium discoideum]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Chiadmi M]]
-[[Category: Chiadmi, M.]]
+[[Category: Janin J]]
-[[Category: Janin, J.]]
+[[Category: Lascu I]]
-[[Category: Lascu, I.]]
+[[Category: Lebras G]]
-[[Category: Lebras, G.]]
+[[Category: Morera S]]
-[[Category: Morera, S.]]
-[[Category: nucleoside triphosphate: nucleoside diphosphate]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:31:36 2007''