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==Crystal structure of malonate occupied DctB==
==Crystal structure of malonate occupied DctB==
<StructureSection load='3e4p' size='340' side='right' caption='[[3e4p]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='3e4p' size='340' side='right'caption='[[3e4p]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3e4p]] 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=3E4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E4P FirstGlance]. <br>
<table><tr><td colspan='2'>[[3e4p]] 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=3E4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E4P FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 2.3&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e4o|3e4o]], [[3e4q|3e4q]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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=3e4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e4p OCA], [https://pdbe.org/3e4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e4p RCSB], [https://www.ebi.ac.uk/pdbsum/3e4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e4p 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=3e4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e4p OCA], [http://pdbe.org/3e4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e4p RCSB], [http://www.ebi.ac.uk/pdbsum/3e4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e4p 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]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3e4p ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3e4p ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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<ref>PMID:18725229</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3e4p" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__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]]
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