5y2v: Difference between revisions

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 ==Strcutrue of the full-length CcmR complexed with 2-OG from Synechocystis PCC6803==
-<StructureSection load='5y2v' size='340' side='right' caption='[[5y2v]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='5y2v' size='340' side='right'caption='[[5y2v]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5y2v]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Syny3 Syny3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y2V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y2V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5y2v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y2V FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.6&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rbcR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1111708 SYNY3])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5y2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y2v OCA], [http://pdbe.org/5y2v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y2v RCSB], [http://www.ebi.ac.uk/pdbsum/5y2v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y2v 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=5y2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y2v OCA], [https://pdbe.org/5y2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y2v RCSB], [https://www.ebi.ac.uk/pdbsum/5y2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y2v ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/P73862_SYNY3 P73862_SYNY3]
-The coordination of carbon and nitrogen metabolism is essential for bacteria to adapt to nutritional variations in the environment, but the underlying mechanism remains poorly understood. In autotrophic cyanobacteria, high CO2 levels favor the carboxylase activity of ribulose 1,5 bisphosphate carboxylase/oxygenase (RuBisCO) to produce 3-phosphoglycerate, whereas low CO2 levels promote the oxygenase activity of RuBisCO, leading to 2-phosphoglycolate (2-PG) production. Thus, the 2-PG level is reversely correlated with that of 2-oxoglutarate (2-OG), which accumulates under a high carbon/nitrogen ratio and acts as a nitrogen-starvation signal. The LysR-type transcriptional repressor NAD(P)H dehydrogenase regulator (NdhR) controls the expression of genes related to carbon metabolism. Based on genetic and biochemical studies, we report here that 2-PG is an inducer of NdhR, while 2-OG is a corepressor, as found previously. Furthermore, structural analyses indicate that binding of 2-OG at the interface between the two regulatory domains (RD) allows the NdhR tetramer to adopt a repressor conformation, whereas 2-PG binding to an intradomain cleft of each RD triggers drastic conformational changes leading to the dissociation of NdhR from its target DNA. We further confirmed the effect of 2-PG or 2-OG levels on the transcription of the NdhR regulon. Together with previous findings, we propose that NdhR can sense 2-OG from the Krebs cycle and 2-PG from photorespiration, two key metabolites that function together as indicators of intracellular carbon/nitrogen status, thus representing a fine sensor for the coordination of carbon and nitrogen metabolism in cyanobacteria.
-Coordinating carbon and nitrogen metabolic signaling through the cyanobacterial global repressor NdhR.,Jiang YL, Wang XP, Sun H, Han SJ, Li WF, Cui N, Lin GM, Zhang JY, Cheng W, Cao DD, Zhang ZY, Zhang CC, Chen Y, Zhou CZ Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):403-408. doi:, 10.1073/pnas.1716062115. Epub 2017 Dec 26. PMID:29279392<ref>PMID:29279392</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5y2v" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Syny3]]
+[[Category: Large Structures]]
-[[Category: Chen, Y]]
+[[Category: Synechocystis sp. PCC 6803 substr. Kazusa]]
-[[Category: Cheng, W]]
+[[Category: Chen Y]]
-[[Category: Han, S J]]
+[[Category: Cheng W]]
-[[Category: Jiang, Y L]]
+[[Category: Han SJ]]
-[[Category: Li, W F]]
+[[Category: Jiang YL]]
-[[Category: Sun, H]]
+[[Category: Li WF]]
-[[Category: Wang, X P]]
+[[Category: Sun H]]
-[[Category: Zhou, C Z]]
+[[Category: Wang XP]]
-[[Category: Lysr-type transcription factor]]
+[[Category: Zhou CZ]]
-[[Category: Transcription]]