2hgv: Difference between revisions

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-{{Seed}}
-[[Image:2hgv.png|left|200px]]
-<!--
+==N-terminal GAF domain of transcriptional pleiotropic repressor CodY==
-The line below this paragraph, containing "STRUCTURE_2hgv", creates the "Structure Box" on the page.
+<StructureSection load='2hgv' size='340' side='right'caption='[[2hgv]], [[Resolution|resolution]] 2.30&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'>[[2hgv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HGV 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene></td></tr>
-{{STRUCTURE_2hgv|  PDB=2hgv  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hgv OCA], [https://pdbe.org/2hgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hgv RCSB], [https://www.ebi.ac.uk/pdbsum/2hgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hgv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CODY_BACSU CODY_BACSU] DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase and sporulation. It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor.<ref>PMID:8830686</ref> <ref>PMID:11331605</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/hg/2hgv_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=2hgv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+CodY is a global regulator of transcription in gram-positive bacteria. It represses during growth genes required for adaptation to nutrient limitation, including virulence genes in some human pathogens. CodY activity is regulated by GTP and branched chain amino acids, metabolites whose intracellular concentrations drop as cells enter stationary phase. Although CodY has a highly conserved sequence, it has no significant similarity to proteins of known structure. Here we report crystal structures of two fragments of CodY from Bacillus subtilis that clearly constitute its cofactor and DNA binding domains and reveal that CodY is a chimera of previously observed folding units. The N-terminal cofactor-binding fragment adopts a fold reminiscent of the GAF domains found in cyclic nucleotide phosphodiesterases and adenylate cyclases. It is a dimer stabilized by an intermolecular six alpha-helical bundle that buries an extensive apolar surface rich in residues invariant in CodY orthologues. The branched chain amino acid ligands reside in hydrophobic pockets of each monomer distal to the dimer-forming surface. The structure of the C-terminal DNA binding domain belongs to the winged helix-turn-helix family. The implications of the structure for DNA binding by CodY and its control by cofactor binding are discussed.
-===N-terminal GAF domain of transcriptional pleiotropic repressor CodY===
+The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria.,Levdikov VM, Blagova E, Joseph P, Sonenshein AL, Wilkinson AJ J Biol Chem. 2006 Apr 21;281(16):11366-73. Epub 2006 Feb 17. PMID:16488888<ref>PMID:16488888</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_16488888}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2hgv" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16488888 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16488888}}
+__TOC__
+</StructureSection>
-==About this Structure==
-HGV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HGV OCA].
-==Reference==
-The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria., Levdikov VM, Blagova E, Joseph P, Sonenshein AL, Wilkinson AJ, J Biol Chem. 2006 Apr 21;281(16):11366-73. Epub 2006 Feb 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16488888 16488888]
-Crystallization of the GTP-dependent transcriptional regulator CodY from Bacillus subtilis., Blagova EV, Levdikov VM, Tachikawa K, Sonenshein AL, Wilkinson AJ, Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):155-7. Epub 2002, Dec 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12499555 12499555]
 [[Category: Bacillus subtilis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Blagova, E V.]]
+[[Category: Blagova EV]]
-[[Category: Levdikov, V M.]]
+[[Category: Levdikov VM]]
-[[Category: Wilkinson, A J.]]
+[[Category: Wilkinson AJ]]
-[[Category: Branched chain amino acid binding]]
-[[Category: Cody]]
-[[Category: Dna-binding]]
-[[Category: Gaf domain]]
-[[Category: Nucleotide-binding]]
-[[Category: Repressor]]
-[[Category: Transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:47:31 2008''