3nek: Difference between revisions

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-[[Image:3nek.png|left|200px]]
-<!--
+==Crystal structure of a nitrogen repressor-like protein MJ0159 from Methanococcus jannaschii==
-The line below this paragraph, containing "STRUCTURE_3nek", creates the "Structure Box" on the page.
+<StructureSection load='3nek' size='340' side='right' caption='[[3nek]], [[Resolution|resolution]] 2.50&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'>[[3nek]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qyx 2qyx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NEK 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"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_3nek|  PDB=3nek  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0159 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3nek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nek OCA], [http://pdbe.org/3nek PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nek RCSB], [http://www.ebi.ac.uk/pdbsum/3nek PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nek 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/ne/3nek_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=3nek ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Plants and microorganisms reduce environmental inorganic nitrogen to ammonium, which then enters various metabolic pathways solely via conversion of 2-oxoglutarate (2OG) to glutamate and glutamine. Cellular 2OG concentrations increase during nitrogen starvation. We recently identified a family of 2OG-sensing proteins--the nitrogen regulatory protein NrpR--that bind DNA and repress transcription of nitrogen assimilation genes. We used X-ray crystallography to determine the structure of NrpR regulatory domain. We identified the NrpR 2OG-binding cleft and show that residues predicted to interact directly with 2OG are conserved among diverse classes of 2OG-binding proteins. We show that high levels of 2OG inhibit NrpRs ability to bind DNA. Electron microscopy analyses document that NrpR adopts different quaternary structures in its inhibited 2OG-bound state compared with its active apo state. Our results indicate that upon 2OG release, NrpR repositions its DNA-binding domains correctly for optimal interaction with DNA thereby enabling gene repression.
-===Crystal structure of a nitrogen repressor-like protein MJ0159 from Methanococcus jannaschii===
+Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.,Wisedchaisri G, Dranow DM, Lie TJ, Bonanno JB, Patskovsky Y, Ozyurt SA, Sauder JM, Almo SC, Wasserman SR, Burley SK, Leigh JA, Gonen T Structure. 2010 Nov 10;18(11):1512-21. PMID:21070950<ref>PMID:21070950</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_21070950}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3nek" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 21070950 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21070950}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Atcc 43067]]
-[[3nek]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qyx 2qyx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NEK OCA].
+[[Category: Almo, S C]]
+[[Category: Bonanno, J B]]
-==Reference==
+[[Category: Burley, S K]]
-<ref group="xtra">PMID:21070950</ref><references group="xtra"/>
+[[Category: Dickey, M]]
-[[Category: Methanocaldococcus jannaschii]]
+[[Category: Koss, J]]
-[[Category: Almo, S C.]]
+[[Category: Malashkevich, V]]
-[[Category: Bonanno, J B.]]
+[[Category: Maletic, M]]
-[[Category: Burley, S K.]]
+[[Category: Structural genomic]]
-[[Category: Dickey, M.]]
+[[Category: Ozyurt, S]]
-[[Category: Koss, J.]]
+[[Category: Patskovsky, Y]]
-[[Category: Malashkevich, V.]]
+[[Category: Rodgers, L]]
-[[Category: Maletic, M.]]
+[[Category: Sauder, J M]]
-[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]
+[[Category: Wu, B]]
-[[Category: Ozyurt, S.]]
+[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
-[[Category: Patskovsky, Y.]]
+[[Category: PSI, Protein structure initiative]]
-[[Category: Rodgers, L.]]
+[[Category: Unknown function]]
-[[Category: Sauder, J M.]]
-[[Category: Wu, B.]]