5n0l: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

The ~~entry~~ 5n0l is ~~ON HOLD until Paper~~ Publication

==The structure of the cofactor binding GAF domain of the nutrient sensor CodY from Clostridium difficile==

== Structural highlights ==

<table><tr><td colspan='2'>[[5n0l]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N0L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N0L FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ILE:ISOLEUCINE'>ILE</scene></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=5n0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n0l OCA], [http://pdbe.org/5n0l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n0l RCSB], [http://www.ebi.ac.uk/pdbsum/5n0l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n0l ProSAT]</span></td></tr>

</table>

== Function ==

[[http://www.uniprot.org/uniprot/A0A031WD25_CLODI A0A031WD25_CLODI]] 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. 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.[HAMAP-Rule:MF_00621]

== 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.

~~Authors~~:

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<ref>PMID:28011634</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased Structures~~]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Blagova, E V]]

[[Category: Levdikov, V M]]

[[Category: Sonenshein, A L]]

[[Category: Wilkinson, A J]]

[[Category: Clostridium]]

[[Category: Gaf domain]]

[[Category: Nutrient sensor]]

[[Category: Transcription]]

[[Category: Transcription regulation]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5n0l is ON HOLD  until Paper Publication
+==The structure of the cofactor binding GAF domain of the nutrient sensor CodY from Clostridium difficile==
+<StructureSection load='5n0l' size='340' side='right' caption='[[5n0l]], [[Resolution|resolution]] 1.68&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5n0l]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N0L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N0L FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ILE:ISOLEUCINE'>ILE</scene></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=5n0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n0l OCA], [http://pdbe.org/5n0l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n0l RCSB], [http://www.ebi.ac.uk/pdbsum/5n0l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n0l ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/A0A031WD25_CLODI A0A031WD25_CLODI]] 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. 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.[HAMAP-Rule:MF_00621]
+<div style="background-color:#fffaf0;">
+== 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.
-Authors:
+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<ref>PMID:28011634</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5n0l" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Blagova, E V]]
+[[Category: Levdikov, V M]]
+[[Category: Sonenshein, A L]]
+[[Category: Wilkinson, A J]]
+[[Category: Clostridium]]
+[[Category: Gaf domain]]
+[[Category: Nutrient sensor]]
+[[Category: Transcription]]
+[[Category: Transcription regulation]]