3gdi: Difference between revisions

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-{{Seed}}
-[[Image:3gdi.jpg|left|200px]]
-<!--
+==Mammalian Clock Protein mPER2 - Crystal Structure of a PAS Domain Fragment==
-The line below this paragraph, containing "STRUCTURE_3gdi", creates the "Structure Box" on the page.
+<StructureSection load='3gdi' size='340' side='right'caption='[[3gdi]], [[Resolution|resolution]] 2.40&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'>[[3gdi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GDI 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]] 2.4&#8491;</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=3gdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gdi OCA], [https://pdbe.org/3gdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gdi RCSB], [https://www.ebi.ac.uk/pdbsum/3gdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gdi ProSAT]</span></td></tr>
-{{STRUCTURE_3gdi|  PDB=3gdi  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PER2_MOUSE PER2_MOUSE] Component of the circadian clock mechanism which is essential for generating circadian rhythms. Negative element in the circadian transcriptional loop. Influences clock function by interacting with other circadian regulatory proteins and transporting them to the nucleus. Negatively regulates CLOCK|NPAS2-BMAL1|BMAL2-induced transactivation.<ref>PMID:10428031</ref> <ref>PMID:17310242</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/gd/3gdi_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=3gdi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+PERIOD proteins are central components of the Drosophila and mammalian circadian clocks. The crystal structure of a Drosophila PERIOD (dPER) fragment comprising two PER-ARNT-SIM (PAS) domains (PAS-A and PAS-B) and two additional C-terminal alpha-helices (alphaE and alphaF) has revealed a homodimer mediated by intermolecular interactions of PAS-A with tryptophane 482 in PAS-B and helix alphaF. Here we present the crystal structure of a monomeric PAS domain fragment of dPER lacking the alphaF helix. Moreover, we have solved the crystal structure of a PAS domain fragment of the mouse PERIOD homologue mPER2. The mPER2 structure shows a different dimer interface than dPER, which is stabilized by interactions of the PAS-B beta-sheet surface including tryptophane 419 (equivalent to Trp482dPER). We have validated and quantitatively analysed the homodimer interactions of dPER and mPER2 by site-directed mutagenesis using analytical gel filtration, analytical ultracentrifugation, and co-immunoprecipitation experiments. Furthermore we show, by yeast-two-hybrid experiments, that the PAS-B beta-sheet surface of dPER mediates interactions with TIMELESS (dTIM). Our study reveals quantitative and qualitative differences between the homodimeric PAS domain interactions of dPER and its mammalian homologue mPER2. In addition, we identify the PAS-B beta-sheet surface as a versatile interaction site mediating mPER2 homodimerization in the mammalian system and dPER-dTIM heterodimer formation in the Drosophila system.
-===Mammalian Clock Protein mPER2 - Crystal Struture of a PAS Domain Fragment===
+Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2.,Hennig S, Strauss HM, Vanselow K, Yildiz O, Schulze S, Arens J, Kramer A, Wolf E PLoS Biol. 2009 Apr 28;7(4):e94. PMID:19402751<ref>PMID:19402751</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3gdi" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19402751}}, adds the Publication Abstract to the page
+*[[Period circadian protein|Period circadian protein]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19402751 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19402751}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-GDI is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GDI OCA].
-==Reference==
-<ref group="xtra">PMID:19402751</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Hennig, S.]]
+[[Category: Hennig S]]
-[[Category: Wolf, E.]]
+[[Category: Wolf E]]
-[[Category: Biological rhythm]]
-[[Category: Cytoplasm]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Tandem pas domain]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 17:06:46 2009''