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| | <StructureSection load='5lnh' size='340' side='right'caption='[[5lnh]], [[Resolution|resolution]] 3.00Å' scene=''> | | <StructureSection load='5lnh' size='340' side='right'caption='[[5lnh]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5lnh]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LNH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LNH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5lnh]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LNH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LNH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 3Å</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> | + | <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=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2gx5|2gx5]], [[2b18|2b18]], [[2hgv|2hgv]], [[2b0l|2b0l]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">codY, BSU16170 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=5lnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lnh OCA], [https://pdbe.org/5lnh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lnh RCSB], [https://www.ebi.ac.uk/pdbsum/5lnh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lnh ProSAT]</span></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=5lnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lnh OCA], [https://pdbe.org/5lnh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lnh RCSB], [https://www.ebi.ac.uk/pdbsum/5lnh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lnh ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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>
| + | [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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| | [[Category: Large Structures]] | | [[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: Cody]]
| + | |
| - | [[Category: Gaf]]
| + | |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transcriptional regulator]]
| + | |
| - | [[Category: Whth]]
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| Structural highlights
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]
Publication Abstract from PubMed
CodY is a branched-chain amino acid (BCAA) and GTP sensor, and a global regulator of transcription in low G + C Gram-positive bacteria. It controls the expression of over 100 genes and operons, principally by repressing during growth genes whose products are required for adaptations to nutrient limitation. CodY consists of a GAF domain that binds BCAAs and a winged helix-turn-helix (wHTH) domain that binds to DNA, but the way in which these domains interact and the structural basis of the BCAA-dependence of this interaction are unknown. To gain new insights, we determined the crystal structure of unliganded CodY from Bacillus subtilis revealing a 10-turn alpha-helix linking otherwise discrete GAF and wHTH domains. The structure of CodY in complex with isoleucine revealed a reorganised GAF domain. In both complexes CodY was tetrameric. Size exclusion chromatography with multiangle laser light scattering (SEC-MALLS) experiments showed that CodY is a dimer at concentrations found in bacterial cells. Comparison of structures of dimers of unliganded CodY and CodY-Ile derived from the tetramers showed a splaying of the wHTH domains when Ile was bound; splaying is likely to account for the increased affinity of Ile-bound CodY for DNA. Electrophoretic mobility shift and SEC-MALLS analyses of CodY binding to 19-36 base-pair operator fragment are consistent with isoleucine-dependent binding of two CodY dimers per duplex. The implications of these observations for effector control of CodY activity are discussed.
Structure of the Branched Chain Amino Acid and GTP Sensing Global Regulator, CodY, from Bacillus subtilis.,Levdikov VM, Blagova EV, Young VL, Belitsky BR, Lebedev A, Sonenshein AL, Wilkinson AJ J Biol Chem. 2016 Dec 23. pii: jbc.M116.754309. doi: 10.1074/jbc.M116.754309. PMID:28011634[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 EV, Young VL, Belitsky BR, Lebedev A, Sonenshein AL, Wilkinson AJ. Structure of the Branched Chain Amino Acid and GTP Sensing Global Regulator, CodY, from Bacillus subtilis. J Biol Chem. 2016 Dec 23. pii: jbc.M116.754309. doi: 10.1074/jbc.M116.754309. PMID:28011634 doi:http://dx.doi.org/10.1074/jbc.M116.754309
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