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| | ==Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy== | | ==Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy== |
| - | <StructureSection load='3qsi' size='340' side='right' caption='[[3qsi]], [[Resolution|resolution]] 3.08Å' scene=''> | + | <StructureSection load='3qsi' size='340' side='right'caption='[[3qsi]], [[Resolution|resolution]] 3.08Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3qsi]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QSI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QSI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3qsi]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QSI 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=SO4:SULFATE+ION'>SO4</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]] 3.08Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HP_1338 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</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=SO4:SULFATE+ION'>SO4</scene></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=3qsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qsi OCA], [http://pdbe.org/3qsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qsi RCSB], [http://www.ebi.ac.uk/pdbsum/3qsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qsi 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=3qsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qsi OCA], [https://pdbe.org/3qsi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qsi RCSB], [https://www.ebi.ac.uk/pdbsum/3qsi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qsi ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY]] Transcriptional regulator (Potential). | + | [https://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY] Transcriptional regulator (Potential). |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Helicobacter pylori NikR (HpNikR) is a nickel-dependent transcription factor that regulates multiple genes in the H. pylori pathogen. There are conflicting data regarding the locations of the Ni(II) sites and the role of Ni(II) coordination in DNA recognition. Herein, we report crystal structures of (i) the metal-binding domain (MBD) of HpNikR (3.08 A) and (ii) a mutant, H74A (2.04 A), designed to disrupt native Ni(II) coordination. In the MBD structure, four nickel ions are coordinated to two different types of nickel sites (4-coordinate, square planar, and 5/6-coordinate, square pyramidal/octahedral). In the H74A structure, all four nickel ions are coordinated to 4-coordinate square-planar sites. DNA-binding studies reveal tighter binding for target DNA sequences for holo-HpNikR compared with the affinities of Ni(II) reconstituted apo-HpNikR and H74A for these same DNA targets, supporting a role for Ni(II) coordination to 5/6 sites in DNA recognition. Small-angle X-ray scattering studies of holo-HpNikR and H74A reveal a high degree of conformational flexibility centered at the DNA-binding domains of H74A, which is consistent with disorder observed in the crystal structure of the protein. A model of DNA recognition by HpNikR is proposed in which Ni(II) coordination to specific sites in the MBD have a long-range effect on the flexibility of the DNA-binding domains and, consequently, the DNA recognition properties.
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| - | Ni(II) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect.,West AL, Evans SE, Gonzalez JM, Carter LG, Tsuruta H, Pozharski E, Michel SL Proc Natl Acad Sci U S A. 2012 Mar 26. PMID:22451934<ref>PMID:22451934</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3qsi" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43504]] | |
| - | [[Category: Gonzalez, J M]] | |
| - | [[Category: Pozharski, E]] | |
| - | [[Category: Dna-binding]] | |
| | [[Category: Helicobacter pylori]] | | [[Category: Helicobacter pylori]] |
| - | [[Category: Metal binding protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Nickel]] | + | [[Category: Gonzalez JM]] |
| - | [[Category: Nikr]] | + | [[Category: Pozharski E]] |
| - | [[Category: Transcription regulator]]
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