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| | ==Crystal Structure of AraR(DBD) in complex with operator ORX1== | | ==Crystal Structure of AraR(DBD) in complex with operator ORX1== |
| - | <StructureSection load='5d4s' size='340' side='right' caption='[[5d4s]], [[Resolution|resolution]] 1.97Å' scene=''> | + | <StructureSection load='5d4s' size='340' side='right'caption='[[5d4s]], [[Resolution|resolution]] 1.97Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5d4s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D4S FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5d4s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D4S FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4egz|4egz]], [[4egy|4egy]], [[4h0e|4h0e]], [[5d4r|5d4r]]</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]] 1.972Å</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=5d4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d4s OCA], [http://pdbe.org/5d4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d4s RCSB], [http://www.ebi.ac.uk/pdbsum/5d4s PDBsum]</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=5d4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d4s OCA], [https://pdbe.org/5d4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d4s RCSB], [https://www.ebi.ac.uk/pdbsum/5d4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d4s ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ARAR_BACSU ARAR_BACSU]] Transcriptional repressor of the arabinose utilization genes. Also regulates its own expression. Binds to two sequences within the promoters of the araABDLMNPQ-abfA operon and the araE gene, and to one sequence in the araR promoter. | + | [https://www.uniprot.org/uniprot/ARAR_BACSU ARAR_BACSU] Transcriptional repressor of the arabinose utilization genes. Also regulates its own expression. Binds to two sequences within the promoters of the araABDLMNPQ-abfA operon and the araE gene, and to one sequence in the araR promoter. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5d4s" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5d4s" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Jain, D]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Nair, D T]] | + | [[Category: Large Structures]] |
| - | [[Category: Narayanan, N]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Arar]] | + | [[Category: Jain D]] |
| - | [[Category: Transcription factor]] | + | [[Category: Nair DT]] |
| - | [[Category: Transcription-dna complex]] | + | [[Category: Narayanan N]] |
| - | [[Category: Winged-helix-turn-helix]]
| + | |
| Structural highlights
Function
ARAR_BACSU Transcriptional repressor of the arabinose utilization genes. Also regulates its own expression. Binds to two sequences within the promoters of the araABDLMNPQ-abfA operon and the araE gene, and to one sequence in the araR promoter.
Publication Abstract from PubMed
Transcription factor-DNA interactions are central to gene regulation. Many transcription factors regulate multiple target genes and can bind sequences that do not conform strictly to the consensus. To understand the structural mechanism utilized by the transcription regulators to bind diverse target sequences, we have employed the repressor AraR from Bacillus subtilis as a model system. AraR is known to bind to eight different operator sites in the bacterial genome. Although there are differences in the sequences of four of these operators, ORE1, ORX1, ORA1, and ORR3, the AraR-DNA binding domain (AraR-DBD) as well as full-length AraR unexpectedly binds to each of these sequences with similar affinities as measured by fluorescence anisotropy experiments. We have determined crystal structures of AraR-DBD in complex with two different natural operators ORE1 and ORX1 up to 2.07 and 1.97 A resolution, respectively. These structures were compared with the previously reported structures of AraR-DBD bound to two other natural operators (ORA1 and ORR3). Interactions of two molecules of AraR-DBD with the symmetric operator, ORE1, are identical, but their interaction with the non-symmetric operator ORX1 results in breakdown of the symmetry in protein-DNA interactions. The novel interactions observed are accompanied by local conformational change in the DNA. ChIP-sequencing (ChIP-Seq) data on other transcription factors has shown that they can bind to diverse targets, and hence the plasticity exhibited by AraR may be a general phenomenon. The ability of transcription factors to form alternate interactions may be important for employment in new functions and evolution of novel regulatory circuits.
Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators.,Jain D, Narayanan N, Nair DT J Biol Chem. 2016 Jan 15;291(3):1235-42. doi: 10.1074/jbc.M115.689695. Epub 2015 , Oct 28. PMID:26511320[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Jain D, Narayanan N, Nair DT. Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators. J Biol Chem. 2016 Jan 15;291(3):1235-42. doi: 10.1074/jbc.M115.689695. Epub 2015 , Oct 28. PMID:26511320 doi:http://dx.doi.org/10.1074/jbc.M115.689695
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