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| ==Structure of the Cytidine Repressor DNA-Binding Domain; an alternate calculation== | | ==Structure of the Cytidine Repressor DNA-Binding Domain; an alternate calculation== |
- | <StructureSection load='2lcv' size='340' side='right' caption='[[2lcv]], [[NMR_Ensembles_of_Models | 11 NMR models]]' scene=''> | + | <StructureSection load='2lcv' size='340' side='right'caption='[[2lcv]], [[NMR_Ensembles_of_Models | 11 NMR models]]' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[2lcv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LCV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LCV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2lcv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LCV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LCV FirstGlance]. <br> |
- | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2l8n|2l8n]]</td></tr> | + | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2l8n|2l8n]]</div></td></tr> |
- | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b3934, cytR, JW3905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b3934, cytR, JW3905 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2lcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lcv OCA], [http://pdbe.org/2lcv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lcv RCSB], [http://www.ebi.ac.uk/pdbsum/2lcv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lcv ProSAT]</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=2lcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lcv OCA], [https://pdbe.org/2lcv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lcv RCSB], [https://www.ebi.ac.uk/pdbsum/2lcv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lcv ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
- | [[http://www.uniprot.org/uniprot/CYTR_ECOLI CYTR_ECOLI]] This protein negatively controls the transcription initiation of genes such as deoCABD, udp, and cdd encoding catabolizing enzymes and nupC, nupG, and tsx encoding transporting and pore-forming proteins. Binds cytidine and adenosine as effectors. | + | [[https://www.uniprot.org/uniprot/CYTR_ECOLI CYTR_ECOLI]] This protein negatively controls the transcription initiation of genes such as deoCABD, udp, and cdd encoding catabolizing enzymes and nupC, nupG, and tsx encoding transporting and pore-forming proteins. Binds cytidine and adenosine as effectors. |
| <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| </StructureSection> | | </StructureSection> |
| [[Category: Ecoli]] | | [[Category: Ecoli]] |
| + | [[Category: Large Structures]] |
| [[Category: Cocco, M J]] | | [[Category: Cocco, M J]] |
| [[Category: Moody, C L]] | | [[Category: Moody, C L]] |
| Structural highlights
Function
[CYTR_ECOLI] This protein negatively controls the transcription initiation of genes such as deoCABD, udp, and cdd encoding catabolizing enzymes and nupC, nupG, and tsx encoding transporting and pore-forming proteins. Binds cytidine and adenosine as effectors.
Publication Abstract from PubMed
The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, in spacing between the recognition half-sites. This suggests a strong likelihood that protein folding would be coupled to DNA binding as a mechanism to accommodate the variety of different operator architectures to which CytR targets. Such coupling is a common feature of sequence-specific DNA-binding proteins including the LacR family repressors; however, there are no significant structural rearrangements upon DNA binding within the three-helix DNA-binding domains (DBDs) studied to date. We used NMR spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue. This structural heterogeneity is previously unknown in the LacR family. These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif. However, this structure differs from all other LacR family members whose structures are known with regard to the packing of the helices and consequently their relative orientations. Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties.
Multiple Conformations of the Cytidine Repressor DNA-Binding Domain Coalesce to One Upon Recognition of a Specific DNA Surface.,Moody CL, Tretyachenko-Ladokhina V, Laue TM, Senear DF, Cocco MJ Biochemistry. 2011 Jun 21. PMID:21688840[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Moody CL, Tretyachenko-Ladokhina V, Laue TM, Senear DF, Cocco MJ. Multiple Conformations of the Cytidine Repressor DNA-Binding Domain Coalesce to One Upon Recognition of a Specific DNA Surface. Biochemistry. 2011 Jun 21. PMID:21688840 doi:10.1021/bi200205v
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