1qw1: Difference between revisions

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 ==Solution Structure of the C-Terminal Domain of DtxR residues 110-226==
-<StructureSection load='1qw1' size='340' side='right'caption='[[1qw1]], [[NMR_Ensembles_of_Models | 14 NMR models]]' scene=''>
+<StructureSection load='1qw1' size='340' side='right'caption='[[1qw1]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1qw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QW1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1qw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QW1 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bym|1bym]], [[1qvp|1qvp]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DTXR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</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=1qw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qw1 OCA], [https://pdbe.org/1qw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qw1 RCSB], [https://www.ebi.ac.uk/pdbsum/1qw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qw1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI]] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.
+[https://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 20: / Line 19: @@
 </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=1qw1 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Diphtheria toxin repressor (DtxR) regulates the expression of iron-sensitive genes in Corynebacterium diphtheriae, including the diphtheria toxin gene. DtxR contains an N-terminal metal- and DNA-binding domain that is connected by a proline-rich flexible peptide segment (Pr) to a C-terminal src homology 3 (SH3)-like domain. We determined the solution structure of the intramolecular complex formed between the proline-rich segment and the SH3-like domain by use of NMR spectroscopy. The structure of the intramolecularly bound Pr segment differs from that seen in eukaryotic prolylpeptide-SH3 domain complexes. The prolylpeptide ligand is bound by the SH3-like domain in a deep crevice lined by aliphatic amino acid residues and passes through the binding site twice but does not adopt a polyprolyl type-II helix. NMR studies indicate that this intramolecular complex is present in the apo-state of the repressor. Isothermal equilibrium denaturation studies show that intramolecular complex formation contributes to the stability of the apo-repressor. The binding affinity of synthetic peptides to the SH3-like domain was determined using isothermal titration calorimetry. From the structure and the binding energies, we calculated the enhancement in binding energy for the intramolecular reaction and compared it to the energetics of dimerization. Together, the structural and biophysical studies suggest that the proline-rich peptide segment of DtxR functions as a switch that modulates the activation of repressor activity.
-Prolylpeptide binding by the prokaryotic SH3-like domain of the diphtheria toxin repressor: a regulatory switch.,Wylie GP, Rangachari V, Bienkiewicz EA, Marin V, Bhattacharya N, Love JF, Murphy JR, Logan TM Biochemistry. 2005 Jan 11;44(1):40-51. PMID:15628844<ref>PMID:15628844</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1qw1" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Diphtheria toxin repressor|Diphtheria toxin repressor]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus diphtheriae kruse in flugge 1886]]
+[[Category: Corynebacterium diphtheriae]]
 [[Category: Large Structures]]
-[[Category: Bienkiewicz, E A]]
+[[Category: Bienkiewicz EA]]
-[[Category: Logan, T M]]
+[[Category: Logan TM]]
-[[Category: Love, J F]]
+[[Category: Love JF]]
-[[Category: Murphy, J R]]
+[[Category: Murphy JR]]
-[[Category: Rangachari, V]]
+[[Category: Rangachari V]]
-[[Category: Wylie, G P]]
+[[Category: Wylie GP]]
-[[Category: C-terminal domain]]
-[[Category: Dtxr]]
-[[Category: Gene regulation]]
-[[Category: Peptide-binding]]
-[[Category: Prokaryotic sh3 domain]]
-[[Category: Repressor]]
-[[Category: Transcription regulation]]