2iu4: Difference between revisions

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-[[Image:2iu4.png|left|200px]]
-<!--
+==Dihydroxyacetone kinase operon co-activator Dha-DhaQ==
-The line below this paragraph, containing "STRUCTURE_2iu4", creates the "Structure Box" on the page.
+<StructureSection load='2iu4' size='340' side='right'caption='[[2iu4]], [[Resolution|resolution]] 1.96&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'>[[2iu4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_lactis"_lister_1873 "bacterium lactis" lister 1873]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IU4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIQ:1-[1,2-DIHYDROXY-1-(HYDROXYMETHYL)ETHYL]-L-HISTIDINE'>HIQ</scene></td></tr>
-{{STRUCTURE_2iu4|  PDB=2iu4  |  SCENE=  }}
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2iu6|2iu6]]</div></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2iu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iu4 OCA], [https://pdbe.org/2iu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iu4 RCSB], [https://www.ebi.ac.uk/pdbsum/2iu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iu4 ProSAT]</span></td></tr>
+</table>
+== 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/iu/2iu4_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=2iu4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Dihydroxyacetone (Dha) kinases are a novel family of kinases with signaling and metabolic functions. Here we report the x-ray structures of the transcriptional activator DhaS and the coactivator DhaQ and characterize their function. DhaQ is a paralog of the Dha binding Dha kinase subunit; DhaS belongs to the family of TetR repressors although, unlike all known members of this family, it is a transcriptional activator. DhaQ and DhaS form a stable complex that in the presence of Dha activates transcription of the Lactococcus lactis dha operon. Dha covalently binds to DhaQ through a hemiaminal bond with a histidine and thereby induces a conformational change, which is propagated to the surface via a cantilever-like structure. DhaS binding protects an inverted repeat whose sequence is GGACACATN6ATTTGTCC and renders two GC base pairs of the operator DNA hypersensitive to DNase I cleavage. The proximal half-site of the inverted repeat partially overlaps with the predicted -35 consensus sequence of the dha promoter.
-===DIHYDROXYACETONE KINASE OPERON CO-ACTIVATOR DHA-DHAQ===
+Regulation of the Dha operon of Lactococcus lactis: a deviation from the rule followed by the Tetr family of transcription regulators.,Christen S, Srinivas A, Bahler P, Zeller A, Pridmore D, Bieniossek C, Baumann U, Erni B J Biol Chem. 2006 Aug 11;281(32):23129-37. Epub 2006 Jun 7. PMID:16760471<ref>PMID:16760471</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16760471}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2iu4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16760471 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16760471}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacterium lactis lister 1873]]
-[[2iu4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IU4 OCA].
-==Reference==
-<ref group="xtra">PMID:016760471</ref><references group="xtra"/>
 [[Category: Glucokinase]]
-[[Category: Lactococcus lactis]]
+[[Category: Large Structures]]
-[[Category: Baumann, U.]]
+[[Category: Baumann, U]]
-[[Category: Christen, S.]]
+[[Category: Christen, S]]
-[[Category: Erni, B.]]
+[[Category: Erni, B]]
-[[Category: Srinivas, A.]]
+[[Category: Srinivas, A]]
 [[Category: Co-activator]]
 [[Category: Dihydroxyacetone]]