1ndl: Difference between revisions

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 ==THE AWD NUCLEOTIDE DIPHOSPHATE KINASE FROM DROSOPHILA==
-<StructureSection load='1ndl' size='340' side='right' caption='[[1ndl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='1ndl' size='340' side='right'caption='[[1ndl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ndl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NDL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ndl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NDL FirstGlance]. <br>
-</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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]] 2.4&#8491;</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=1ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndl OCA], [http://pdbe.org/1ndl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ndl RCSB], [http://www.ebi.ac.uk/pdbsum/1ndl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ndl ProSAT]</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=1ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndl OCA], [https://pdbe.org/1ndl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ndl RCSB], [https://www.ebi.ac.uk/pdbsum/1ndl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ndl ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NDKA_DROME NDKA_DROME]] 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.<ref>PMID:2849580</ref> <ref>PMID:2175255</ref> <ref>PMID:7559441</ref>
+[https://www.uniprot.org/uniprot/NDKA_DROME NDKA_DROME] 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.<ref>PMID:2849580</ref> <ref>PMID:2175255</ref> <ref>PMID:7559441</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/nd/1ndl_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1ndl_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 19: @@
 </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=1ndl ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-BACKGROUND: Nucleotide diphosphate kinase (NDP kinase) is a phosphate transfer enzyme involved in cell regulation and in animal development. Drosophila NDP kinase is the product of the abnormal wing disc (awd) developmental gene, a point mutation in which can produce the killer of prune (K-pn) conditional lethal phenotype. The highly homologous mammalian genes control metastasis and a human NDP kinase acts as a transcription factor. RESULTS: The X-ray structure of the Awd protein prepared from Drosophila was solved at 2.4 A resolution by molecular replacement from the homologous Dictyostelium protein. Both are hexamers, and both have the same fold and the same active site. Subunit contacts differ as a result of sequence changes in the carboxy-terminal segment and in the loop that is the site of the K-pn mutation. CONCLUSIONS: Regulatory properties of animal NDP kinases depend on interactions with other macromolecules, such as DNA and the product of the Drosophila prune gene. The Awd structure suggests an allosteric mechanism of action of NDP kinase where DNA is the effector and the protein undergoes a major conformational change, possibly dissociating to dimers.
-Crystal structure of the Awd nucleotide diphosphate kinase from Drosophila.,Chiadmi M, Morera S, Lascu I, Dumas C, Le Bras G, Veron M, Janin J Structure. 1993 Dec 15;1(4):283-93. PMID:8081741<ref>PMID:8081741</ref>
+==See Also==
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1ndl" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Drome]]
+[[Category: Drosophila melanogaster]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Large Structures]]
-[[Category: Chiadmi, M]]
+[[Category: Chiadmi M]]
-[[Category: Dumas, C]]
+[[Category: Dumas C]]
-[[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: Veron, M]]
+[[Category: Veron M]]
-[[Category: Phosphotransferase]]