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| | ==Crystal structure of apo DctB== | | ==Crystal structure of apo DctB== |
| - | <StructureSection load='3e4q' size='340' side='right' caption='[[3e4q]], [[Resolution|resolution]] 2.75Å' scene=''> | + | <StructureSection load='3e4q' size='340' side='right'caption='[[3e4q]], [[Resolution|resolution]] 2.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3e4q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E4Q FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3e4q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E4Q FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.75Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e4o|3e4o]], [[3e4p|3e4p]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dctB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</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=3e4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e4q OCA], [https://pdbe.org/3e4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e4q RCSB], [https://www.ebi.ac.uk/pdbsum/3e4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e4q ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </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=3e4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e4q OCA], [http://pdbe.org/3e4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e4q RCSB], [http://www.ebi.ac.uk/pdbsum/3e4q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e4q ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DCTB_RHIME DCTB_RHIME]] Member of the two-component regulatory system DctB/DctD involved in the transport of C4-dicarboxylates. DctB functions as a membrane-associated protein kinase that phosphorylates DctD in response to environmental signals. | + | [https://www.uniprot.org/uniprot/DCTB_RHIME DCTB_RHIME] Member of the two-component regulatory system DctB/DctD involved in the transport of C4-dicarboxylates. DctB functions as a membrane-associated protein kinase that phosphorylates DctD in response to environmental signals. |
| | == 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/e4/3e4q_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e4/3e4q_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: Atcc 9930]] | + | [[Category: Large Structures]] |
| - | [[Category: Histidine kinase]] | + | [[Category: Sinorhizobium meliloti]] |
| - | [[Category: Liang, Y H]] | + | [[Category: Liang YH]] |
| - | [[Category: Nan, B Y]] | + | [[Category: Nan BY]] |
| - | [[Category: Nan, J]] | + | [[Category: Nan J]] |
| - | [[Category: Panjikar, S]] | + | [[Category: Panjikar S]] |
| - | [[Category: Su, X D]] | + | [[Category: Su XD]] |
| - | [[Category: Zhou, Y F]] | + | [[Category: Zhou YF]] |
| - | [[Category: N-term helical dimerization domain]]
| + | |
| - | [[Category: Pas domain]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
DCTB_RHIME Member of the two-component regulatory system DctB/DctD involved in the transport of C4-dicarboxylates. DctB functions as a membrane-associated protein kinase that phosphorylates DctD in response to environmental signals.
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
C(4)-dicarboxylates are the major carbon and energy sources during the symbiotic growth of rhizobia. Responses to C(4)-dicarboxylates depend on typical two-component systems (TCS) consisting of a transmembrane sensor histidine kinase and a cytoplasmic response regulator. The DctB-DctD system is the first identified TCS for C(4)-dicarboxylates sensing. Direct ligand binding to the sensor domain of DctB is believed to be the first step of the sensing events. In this report, the water-soluble periplasmic sensor domain of Sinorhizobium meliloti DctB (DctBp) was studied, and three crystal structures were solved: the apo protein, a complex with C(4) succinate, and a complex with C(3) malonate. Different from the two structurally known CitA family of carboxylate sensor proteins CitA and DcuS, the structure of DctBp consists of two tandem Per-Arnt-Sim (PAS) domains and one N-terminal helical region. Only the membrane-distal PAS domain was found to bind the ligands, whereas the proximal PAS domain was empty. Comparison of DctB, CitA, and DcuS suggests a detailed stereochemistry of C(4)-dicarboxylates ligand perception. The structures of the different ligand binding states of DctBp also revealed a series of conformational changes initiated upon ligand binding and propagated to the N-terminal domain responsible for dimerization, providing insights into understanding the detailed mechanism of the signal transduction of TCS histidine kinases.
C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain.,Zhou YF, Nan B, Nan J, Ma Q, Panjikar S, Liang YH, Wang Y, Su XD J Mol Biol. 2008 Oct 31;383(1):49-61. Epub 2008 Aug 12. PMID:18725229[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zhou YF, Nan B, Nan J, Ma Q, Panjikar S, Liang YH, Wang Y, Su XD. C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain. J Mol Biol. 2008 Oct 31;383(1):49-61. Epub 2008 Aug 12. PMID:18725229 doi:10.1016/j.jmb.2008.08.010
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