1f5t: Difference between revisions

Revision as of 15:56, 2 May 2008

DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE

OverviewOverview

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.

About this StructureAbout this Structure

1F5T is a Single protein structure of sequence from Corynebacterium diphtheriae. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Fri May 2 15:56:07 2008

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OCA

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 [[Image:1f5t.gif|left|200px]]
- {{Structure
+<!--
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+The line below this paragraph, containing "STRUCTURE_1f5t", creates the "Structure Box" on the page.
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+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>
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-|RESOURCES=<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://www.ebi.ac.uk/pdbsum/1f5t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1f5t RCSB]</span>
-}}
 '''DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE'''
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 [[Category: Ringe, D.]]
 [[Category: White, A.]]
-[[Category: diphtheria tox repressor]]
+[[Category: Diphtheria tox repressor]]
-[[Category: dna-binding regulatory protein]]
+[[Category: Dna-binding regulatory protein]]
-[[Category: dna-protein complex]]
+[[Category: Dna-protein complex]]
-[[Category: helix-turn-helix motif]]
+[[Category: Helix-turn-helix motif]]
-[[Category: iron-regulated repressor]]
+[[Category: Iron-regulated repressor]]
-[[Category: transcription regulator]]
+[[Category: Transcription regulator]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 15:56:07 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:16:37 2008''