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| | ==Crystal Structure of DtxR(M10A C102D) Complexed with Nickel(II)== | | ==Crystal Structure of DtxR(M10A C102D) Complexed with Nickel(II)== |
| - | <StructureSection load='2qqb' size='340' side='right' caption='[[2qqb]], [[Resolution|resolution]] 1.92Å' scene=''> | + | <StructureSection load='2qqb' size='340' side='right'caption='[[2qqb]], [[Resolution|resolution]] 1.92Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2qqb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QQB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QQB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2qqb]] is a 1 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=2QQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QQB 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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.92Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xcv|1xcv]], [[1p92|1p92]], [[1ddn|1ddn]], [[2tdx|2tdx]], [[2qq9|2qq9]], [[2qqa|2qqa]]</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dtxR ([http://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=2qqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qqb OCA], [https://pdbe.org/2qqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qqb RCSB], [https://www.ebi.ac.uk/pdbsum/2qqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qqb ProSAT]</span></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=2qqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qqb OCA], [http://pdbe.org/2qqb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qqb RCSB], [http://www.ebi.ac.uk/pdbsum/2qqb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qqb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus diphtheriae kruse in flugge 1886]] | + | [[Category: Corynebacterium diphtheriae]] |
| - | [[Category: Aquino, J A.D]] | + | [[Category: Large Structures]] |
| - | [[Category: Aquino, K E.D]] | + | [[Category: D'Aquino JA]] |
| - | [[Category: Denninger, A]] | + | [[Category: D'Aquino KE]] |
| - | [[Category: Lattimer, J R]]
| + | [[Category: Denninger A]] |
| - | [[Category: Ringe, D]]
| + | [[Category: Lattimer JR]] |
| - | [[Category: Activation]] | + | [[Category: Ringe D]] |
| - | [[Category: Cytoplasm]] | + | |
| - | [[Category: Dna-binding]] | + | |
| - | [[Category: Dtxr]]
| + | |
| - | [[Category: Ferrous iron]]
| + | |
| - | [[Category: Helix-turn-helix]]
| + | |
| - | [[Category: Metal ion]]
| + | |
| - | [[Category: Regulator]]
| + | |
| - | [[Category: Repressor]]
| + | |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transcription regulation]]
| + | |
| - | [[Category: Transcription regulator]]
| + | |
| Structural highlights
Function
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
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The metal ion-regulated transcriptional repressor DtxR has been shown to repress the transcription of the diphtheria toxin and other genes associated with ferrous ion homeostasis in Corynebacterium diphtheriae. In vivo studies of single-alanine mutations located in the N-terminal helix of DtxR show that the activity of the mutants is reduced compared to that of the wild type. The three-dimensional structures of the apo and activated forms of DtxR show conformational changes in the N-terminal helix resulting from metal ion activation. We have studied the N-terminal helix mutants DtxR(D6A,C102D), DtxR(E9A,C102D), and DtxR(M10A,C102D) using crystallographic and calorimetric techniques to gain insight into the possible reasons for such behavior at a molecular level. The binding affinities for metal ion extracted from the calorimetric titrations of the mutants DtxR(D6A,C102D) and DtxR(E9A,C102D) are very similar to those found for DtxR(C102D), while the same experiments performed with the mutant DtxR(M10A,C102D), bearing the M10A mutation located in binding site 2, show a decreased binding affinity in a predictable fashion. These results suggest that the decreased activity observed in these mutants cannot be explained exclusively by changes in the binding affinity of the repressor. The crystal structures of Ni-DtxR(M10A,C102D), Ni-DtxR(E9A,C102D), and Ni-DtxR(D6A,C102D) clearly show the presence of two metal ions bound. In the structure of Ni-DtxR(M10A,C102D), a water replaces Met10 in binding site 2. In the structure of Ni-DtxR(D6A,C102D), the nonhelical conformation of the N-terminal region characteristic of the activated form is absent. The side chain of Asp6 is critical in stabilization of the nonhelical conformation. This conformation is identical in all high-resolution structures of activated DtxR with an intact N-terminal helix, suggesting relevance in DtxR's regulatory function.
Role of the N-terminal helix in the metal ion-induced activation of the diphtheria toxin repressor DtxR.,D'Aquino JA, Lattimer JR, Denninger A, D'Aquino KE, Ringe D Biochemistry. 2007 Oct 23;46(42):11761-70. Epub 2007 Sep 29. PMID:17902703[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ D'Aquino JA, Lattimer JR, Denninger A, D'Aquino KE, Ringe D. Role of the N-terminal helix in the metal ion-induced activation of the diphtheria toxin repressor DtxR. Biochemistry. 2007 Oct 23;46(42):11761-70. Epub 2007 Sep 29. PMID:17902703 doi:http://dx.doi.org/10.1021/bi7007883
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