2hur: Difference between revisions

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-[[Image:2hur.png|left|200px]]
-<!--
+==Escherichia coli nucleoside diphosphate kinase==
-The line below this paragraph, containing "STRUCTURE_2hur", creates the "Structure Box" on the page.
+<StructureSection load='2hur' size='340' side='right'caption='[[2hur]], [[Resolution|resolution]] 1.62&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2hur]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HUR FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.62&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2hur|  PDB=2hur  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hur OCA], [https://pdbe.org/2hur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hur RCSB], [https://www.ebi.ac.uk/pdbsum/2hur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hur ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDK_ECOLI NDK_ECOLI] 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.[HAMAP-Rule:MF_00451]
+== 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/hu/2hur_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=2hur ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nucleoside diphosphate kinase (NDPK) catalyzes the transfer of gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. The subunit folding and the dimeric basic structural unit are remarkably the same for available structures but, depending on species, dimers self-associate to form hexamers or tetramers. The crystal structure of the Escherichia coli NDPK reveals a new tetrameric quaternary structure for this protein family. The two tetramers differ by the relative orientation of interacting dimers, which face either the convex or the concave side of their central sheet as in either Myxococcus xanthus (type I) or E. coli (type II), respectively. In the type II tetramer, the subunits interact by a new interface harboring a zone called the Kpn loop as in hexamers, but by the opposite face of this loop. The evolutionary conservation of the interface residues indicates that this new quaternary structure seems to be the most frequent assembly mode in bacterial tetrameric NDP kinases.
-===Escherichia coli nucleoside diphosphate kinase===
+The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family.,Moynie L, Giraud MF, Georgescauld F, Lascu I, Dautant A Proteins. 2007 May 15;67(3):755-65. PMID:17330300<ref>PMID:17330300</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2hur" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17330300}}, adds the Publication Abstract to the page
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17330300 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17330300}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[2hur]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HUR OCA].
-==Reference==
-<ref group="xtra">PMID:17330300</ref><ref group="xtra">PMID:7730286</ref><ref group="xtra">PMID:8263923</ref><ref group="xtra">PMID:7966307</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Large Structures]]
-[[Category: Dautant, A.]]
+[[Category: Dautant A]]
-[[Category: Georgescauld, F.]]
+[[Category: Georgescauld F]]
-[[Category: Giraud, M F.]]
+[[Category: Giraud M-F]]
-[[Category: Lascu, I.]]
+[[Category: Lascu I]]
-[[Category: Moynie, L.]]
+[[Category: Moynie L]]
-[[Category: Signaling protein]]
-[[Category: Transferase]]
-[[Category: Type ii tetramer]]