2b0l: Difference between revisions

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[[Image:2b0l.gif|left|200px]]


{{Structure
==C-terminal DNA binding domain of transcriptional pleiotropic repressor CodY.==
|PDB= 2b0l |SIZE=350|CAPTION= <scene name='initialview01'>2b0l</scene>, resolution 2.90&Aring;
<StructureSection load='2b0l' size='340' side='right'caption='[[2b0l]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[2b0l]] is a 3 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=2B0L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B0L FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
|GENE= codY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b0l OCA], [https://pdbe.org/2b0l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b0l RCSB], [https://www.ebi.ac.uk/pdbsum/2b0l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b0l ProSAT]</span></td></tr>
}}
</table>
 
== Function ==
'''C-terminal DNA binding domain of transcriptional pleiotropic repressor CodY.'''
[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]]
==Overview==
Check<jmol>
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.
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b0/2b0l_consurf.spt"</scriptWhenChecked>
==About this Structure==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
2B0L 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=2B0L OCA].  
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
==Reference==
</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=2b0l ConSurf].
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]
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Blagova, E.]]
[[Category: Blagova E]]
[[Category: Joseph, P.]]
[[Category: Joseph P]]
[[Category: Levdikov, V M.]]
[[Category: Levdikov VM]]
[[Category: Sonenshein, A L.]]
[[Category: Sonenshein AL]]
[[Category: Wilkinson, A J.]]
[[Category: Wilkinson AJ]]
[[Category: cody]]
[[Category: dna-binding; nucleotide-binding; repressor; transcription regulation; winged hth motif.]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:56:08 2008''

Latest revision as of 09:15, 14 February 2024

C-terminal DNA binding domain of transcriptional pleiotropic repressor CodY.

2b0l, resolution 2.90Å

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