1f5t: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE==
-<StructureSection load='1f5t' size='340' side='right' caption='[[1f5t]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='1f5t' size='340' side='right'caption='[[1f5t]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1f5t]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1f5t]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F5T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 3&#8491;</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=1f5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5t OCA], [http://pdbe.org/1f5t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f5t RCSB], [http://www.ebi.ac.uk/pdbsum/1f5t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f5t ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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=1f5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5t OCA], [https://pdbe.org/1f5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f5t RCSB], [https://www.ebi.ac.uk/pdbsum/1f5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f5t ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/1f5t_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/1f5t_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 20: @@
 </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=1f5t ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The expression of diphtheria toxin is controlled by the diphtheria toxin repressor (DtxR). Under conditions of high iron concentration, DtxR binds the tox operator to inhibit transcription. To study how DNA binding specificity is achieved by this repressor, we solved the crystal structure of the nickel(II) activated DtxR(C102D) mutant complexed with a 43mer DNA duplex containing the DtxR consensus binding sequence. Structural analysis of this complex and comparison with a previously determined DtxR(C102D)-Ni(II)-tox operator ternary complex revealed unusual van der Waals interactions between Ser37/Pro39 of the repressor helix-turn-helix (HTH) motif and the methyl groups of specific thymine bases in the consensus binding sequence. Gel mobility shift assays utilizing deoxyuridine modified duplex DNA probes proved the importance of these interactions: the four methyl groups shown to interact with Ser37/Pro39 in the crystal structure contribute a total of 3.4 kcal/mol to binding energy. Thus, in addition to making base-specific hydrogen-bonding interactions to the DNA through its Gln43 residue, DtxR also recognizes methyl groups at certain positions in the DNA sequence with its Ser37 and Pro39 side chains, to achieve binding specificity toward its cognate operator sequences.
-Methyl groups of thymine bases are important for nucleic acid recognition by DtxR.,Chen CS, White A, Love J, Murphy JR, Ringe D Biochemistry. 2000 Aug 29;39(34):10397-407. PMID:10956029<ref>PMID:10956029</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1f5t" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Diphtheria toxin repressor|Diphtheria toxin repressor]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Chen, S]]
+[[Category: Corynebacterium diphtheriae]]
-[[Category: Love, J]]
+[[Category: Large Structures]]
-[[Category: Murphy, J R]]
+[[Category: Chen S]]
-[[Category: Ringe, D]]
+[[Category: Love J]]
-[[Category: White, A]]
+[[Category: Murphy JR]]
-[[Category: Diphtheria tox repressor]]
+[[Category: Ringe D]]
-[[Category: Dna-binding regulatory protein]]
+[[Category: White A]]
-[[Category: Dna-protein complex]]
-[[Category: Helix-turn-helix motif]]
-[[Category: Iron-regulated repressor]]
-[[Category: Transcription regulator]]
-[[Category: Transcription-dna complex]]