6g8h: Difference between revisions

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 <StructureSection load='6g8h' size='340' side='right'caption='[[6g8h]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6g8h]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6G8H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6g8h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_USDA_110 Bradyrhizobium diazoefficiens USDA 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6G8H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CWE:R-naringenin'>CWE</scene>, <scene name='pdbligand=NAR:NARINGENIN'>NAR</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</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='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=CWE:(2~{R})-2-(4-hydroxyphenyl)-5,7-bis(oxidanyl)-2,3-dihydrochromen-4-one'>CWE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAR:NARINGENIN'>NAR</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</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;'>[[6g87|6g87]]</div></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=6g8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g8h OCA], [https://pdbe.org/6g8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6g8h RCSB], [https://www.ebi.ac.uk/pdbsum/6g8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6g8h ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q89M71_BRADU Q89M71_BRADU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
-Previous microarray analyses revealed that in Bradyrhizobium japonicum, about 100 genes are induced by genistein, an isoflavonoid secreted by soybean. This includes the three genes freC, freA, and freB (systematic designations bll4319, bll4320, and bll4321), which are likely to form a genistein-, daidzein-, and coumestrol-inducible operon and to encode a multidrug efflux system. Upstream of freCAB and in the opposite orientation, FrrA (systematic designation Blr4322), which has similarity to TetR-type regulators, is encoded. A deletion of frrA leads to increased expression of freB in the absence of an inducer. We identified the correct translational start codon of frrA and showed that the gene is inducible by genistein and daidzein. The protein, which was heterologously expressed and purified from Escherichia coli, binds to two palindrome-like DNA elements (operator A and operator B), which are located in the intergenic region between freC and frrA. The replacement of several nucleotides or the insertion of additional spacer nucleotides prevented binding. Binding of FrrA was also affected by the addition of genistein. By mapping the transcription start sites, we found that operator A covers the transcriptional start site of freC and operator B is probably located between the -35 regions of the two divergently oriented genes. Operator A seems to be conserved in a few similar gene constellations in other proteobacteria. Our data indicate that in B. japonicum, besides NodD1 (the LysR family) and NodVW (a two-component response regulator), a third regulator type (a TetR family member) which responds to the plant signal molecules genistein and daidzein exists.
+Bradyrhizobium diazoefficiens, a bacterial symbiont of soybean and other leguminous plants, enters a nodulation-promoting genetic programme in the presence of host-produced flavonoids and related signalling compounds. Here, we describe the crystal structure of an isoflavonoid-responsive regulator (FrrA) from Bradyrhizobium, as well as cocrystal structures with inducing and noninducing ligands (genistein and naringenin, respectively). The structures reveal a TetR-like fold whose DNA-binding domain is capable of adopting a range of orientations. A single molecule of either genistein or naringenin is asymmetrically bound in a central cavity of the FrrA homodimer, mainly via C-H contacts to the pi-system of the ligands. Strikingly, however, the interaction does not provoke any conformational changes in the repressor. Both the flexible positioning of the DNA-binding domain and the absence of structural change upon ligand binding are corroborated by small-angle X-ray scattering (SAXS) experiments in solution. Together with a model of the promoter-bound state of FrrA our results suggest that inducers act as a wedge, preventing the DNA-binding domains from moving close enough together to interact with successive positions of the major groove of the palindromic operator.
-Characterization of the flavonoid-responsive regulator FrrA and its binding sites.,Wenzel M, Lang K, Gunther T, Bhandari A, Weiss A, Lulchev P, Szentgyorgyi E, Kranzusch B, Gottfert M J Bacteriol. 2012 May;194(9):2363-70. doi: 10.1128/JB.06567-11. Epub 2012 Mar 2. PMID:22389485<ref>PMID:22389485</ref>
+The induction mechanism of the flavonoid-responsive regulator FrrA.,Werner N, Werten S, Hoppen J, Palm GJ, Gottfert M, Hinrichs W FEBS J. 2021 Jul 27. doi: 10.1111/febs.16141. PMID:34314575<ref>PMID:34314575</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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 __TOC__
 </StructureSection>
+[[Category: Bradyrhizobium diazoefficiens USDA 110]]
 [[Category: Large Structures]]
-[[Category: Goettfert, M]]
+[[Category: Goettfert M]]
-[[Category: Hinrichs, W]]
+[[Category: Hinrichs W]]
-[[Category: Hoppen, J]]
+[[Category: Hoppen J]]
-[[Category: Palm, G]]
+[[Category: Palm G]]
-[[Category: Werner, N]]
+[[Category: Werner N]]
-[[Category: Werten, S]]
+[[Category: Werten S]]
-[[Category: Flavonoid]]
-[[Category: Repressor]]
-[[Category: Tetr-family]]
-[[Category: Transcription]]