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==Crystal structure of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291 - CdPadR_0991 to 1.89 Angstrom resolution==
<StructureSection load='5dym' size='340' side='right'caption='[[5dym]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5dym]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile_R20291 Clostridioides difficile R20291]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DYM FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.894&#8491;</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=5dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dym OCA], [https://pdbe.org/5dym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dym RCSB], [https://www.ebi.ac.uk/pdbsum/5dym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dym ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
BACKGROUND: Clostridium difficile is a spore-forming obligate anaerobe that can remain viable for extended periods, even in the presence of antibiotics, which contributes to the persistence of this bacterium as a human pathogen during host-to-host transmission and in hospital environments. We examined the structure and function of a gene product with the locus tag CDR20291_0991 (cdPadR1) as part of our broader goal aimed at elucidating transcription regulatory mechanisms involved in virulence and antibiotic resistance of the recently emergent hypervirulent C. difficile strain R20291. cdPadR1 is genomically positioned near genes that are involved in stress response and virulence. In addition, it was previously reported that cdPadR1 and a homologue from the historical C. difficile strain 630 (CD630_1154) were differentially expressed when exposed to stressors, including antibiotics. RESULTS: The crystal structure of cdPadR1 was determined to 1.9 A resolution, which revealed that it belongs to the PadR-s2 subfamily of PadR transcriptional regulators. cdPadR1 binds its own promoter and other promoter regions from within the C. difficile R20291 genome. DNA binding experiments demonstrated that cdPadR1 binds a region comprised of inverted repeats and an AT-rich core with the predicted specific binding motif, GTACTAT(N2)ATTATA(N)AGTA, within its own promoter that is also present in 200 other regions in the C. difficile R20291 genome. Mutation of the highly conserved W in alpha4 of the effector binding/oligomerization domain, which is predicted to be involved in multi-drug recognition and dimerization in other PadR-s2 proteins, resulted in alterations of cdPadR1 binding to the predicted binding motif, potentially due to loss of higher order oligomerization. CONCLUSIONS: Our results indicate that cdPadR1 binds a region within its own promoter consisting of the binding motif GTACTAT(N2)ATTATA(N)AGTA and seems to associate non-specifically with longer DNA fragments in vitro, which may facilitate promoter and motif searching. This suggests that cdPadR1 acts as a transcriptional auto-regulator, binding specific sites within its own promoter, and is part of a broad gene regulatory network involved, in part, with environmental stress response, antibiotic resistance and virulence.

Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291.,Isom CE, Menon SK, Thomas LM, West AH, Richter-Addo GB, Karr EA BMC Microbiol. 2016 Oct 4;16(1):231. PMID:27716049<ref>PMID:27716049</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Clostridioides difficile R20291]]
[[Category: Large Structures]]
[[Category: Isom CE]]
[[Category: Karr EA]]
[[Category: Menon SK]]
[[Category: Richter-Addo GB]]
[[Category: West AH]]