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| | ==N-terminal GAF domain of transcriptional pleiotropic repressor CodY== | | ==N-terminal GAF domain of transcriptional pleiotropic repressor CodY== |
| - | <StructureSection load='2gx5' size='340' side='right' caption='[[2gx5]], [[Resolution|resolution]] 1.74Å' scene=''> | + | <StructureSection load='2gx5' size='340' side='right'caption='[[2gx5]], [[Resolution|resolution]] 1.74Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2gx5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GX5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GX5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2gx5]] is a 4 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=2GX5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GX5 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PCG:CYCLIC+GUANOSINE+MONOPHOSPHATE'>PCG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.74Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2b18|2b18]], [[2b0l|2b0l]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PCG:CYCLIC+GUANOSINE+MONOPHOSPHATE'>PCG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">codY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2gx5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gx5 OCA], [https://pdbe.org/2gx5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gx5 RCSB], [https://www.ebi.ac.uk/pdbsum/2gx5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gx5 ProSAT]</span></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=2gx5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gx5 OCA], [http://pdbe.org/2gx5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gx5 RCSB], [http://www.ebi.ac.uk/pdbsum/2gx5 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/2gx5_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/2gx5_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus globigii migula 1900]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Blagova, E V]] | + | [[Category: Large Structures]] |
| - | [[Category: Levdikov, V M]] | + | [[Category: Blagova EV]] |
| - | [[Category: Wilkinson, A J]] | + | [[Category: Levdikov VM]] |
| - | [[Category: Branched chain amino acid binding]] | + | [[Category: Wilkinson AJ]] |
| - | [[Category: Cody]]
| + | |
| - | [[Category: Dna-binding]]
| + | |
| - | [[Category: Gaf domain]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Repressor]]
| + | |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transcription regulation]]
| + | |
| Structural highlights
2gx5 is a 4 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.74Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Serror P, Sonenshein AL. CodY is required for nutritional repression of Bacillus subtilis genetic competence. J Bacteriol. 1996 Oct;178(20):5910-5. PMID:8830686
- ↑ Ratnayake-Lecamwasam M, Serror P, Wong KW, Sonenshein AL. Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev. 2001 May 1;15(9):1093-103. PMID:11331605 doi:http://dx.doi.org/10.1101/gad.874201
- ↑ Levdikov VM, Blagova E, Joseph P, Sonenshein AL, Wilkinson AJ. The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria. J Biol Chem. 2006 Apr 21;281(16):11366-73. Epub 2006 Feb 17. PMID:16488888 doi:http://dx.doi.org/10.1074/jbc.M513015200
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