2it0

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(New page: 200px<br /><applet load="2it0" size="450" color="white" frame="true" align="right" spinBox="true" caption="2it0, resolution 2.600&Aring;" /> '''Crystal structure o...)
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[[Image:2it0.gif|left|200px]]<br /><applet load="2it0" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2it0, resolution 2.600&Aring;" />
 
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'''Crystal structure of a two-domain IdeR-DNA complex crystal form II'''<br />
 
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==Overview==
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==Crystal structure of a two-domain IdeR-DNA complex crystal form II==
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The iron-dependent regulator IdeR is a key transcriptional regulator of, iron uptake in Mycobacterium tuberculosis. In order to increase our, insight into the role of the SH3-like third domain of this essential, regulator, the metal-binding and DNA-binding properties of two-domain IdeR, (2D-IdeR) whose SH3-like domain has been truncated were characterized. The, equilibrium dissociation constants for Co2+ and Ni2+ activation of 2D-IdeR, for binding to the fxbA operator and the DNA-binding affinities of 2D-IdeR, in the presence of excess metal ions were estimated using fluorescence, spectroscopy. 2D-IdeR binds to fxbA operator DNA with similar affinity as, full-length IdeR in the presence of excess metal ion. However, the Ni2+, concentrations required to activate 2D-IdeR for DNA binding appear to be, smaller than that for full-length IdeR while the concentration of Co2+, required for activation remains the same. We have determined the crystal, structures of Ni2+-activated 2D-IdeR at 1.96 A resolution and its double, dimer complex with the mbtA-mbtB operator DNA in two crystal forms at 2.4, A and 2.6 A, the highest resolutions for DNA complexes for any structures, of iron-dependent regulator family members so far. The 2D-IdeR-DNA complex, structures confirm the specificity of Ser37 and Pro39 for thymine bases, and suggest preferential contacts of Gln43 to cytosine bases of the DNA., In addition, our 2D-IdeR structures reveal a remarkable property of the, TEV cleavage sequence remaining after removal of the C-terminal His6. This, C-terminal tail promotes crystal contacts by forming a beta-sheet with the, corresponding tail of neighboring subunits in two unrelated structures of, 2D-IdeR, one with and one without DNA. The contact-promoting properties of, this C-terminal TEV cleavage sequence may be beneficial for crystallizing, other proteins.
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<StructureSection load='2it0' size='340' side='right'caption='[[2it0]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2it0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IT0 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2it0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2it0 OCA], [https://pdbe.org/2it0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2it0 RCSB], [https://www.ebi.ac.uk/pdbsum/2it0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2it0 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/IDER_MYCTU IDER_MYCTU] Metal-dependent DNA-binding protein that controls transcription of many genes involved in iron metabolism. Acts as a repressor of siderophore biosynthesis and as a positive modulator of iron storage. Also regulates expression of transporters, proteins involved in siderophore synthesis, iron storage and transcriptional regulators.<ref>PMID:11722747</ref> <ref>PMID:12065475</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/2it0_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2it0 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The iron-dependent regulator IdeR is a key transcriptional regulator of iron uptake in Mycobacterium tuberculosis. In order to increase our insight into the role of the SH3-like third domain of this essential regulator, the metal-binding and DNA-binding properties of two-domain IdeR (2D-IdeR) whose SH3-like domain has been truncated were characterized. The equilibrium dissociation constants for Co2+ and Ni2+ activation of 2D-IdeR for binding to the fxbA operator and the DNA-binding affinities of 2D-IdeR in the presence of excess metal ions were estimated using fluorescence spectroscopy. 2D-IdeR binds to fxbA operator DNA with similar affinity as full-length IdeR in the presence of excess metal ion. However, the Ni2+ concentrations required to activate 2D-IdeR for DNA binding appear to be smaller than that for full-length IdeR while the concentration of Co2+ required for activation remains the same. We have determined the crystal structures of Ni2+-activated 2D-IdeR at 1.96 A resolution and its double dimer complex with the mbtA-mbtB operator DNA in two crystal forms at 2.4 A and 2.6 A, the highest resolutions for DNA complexes for any structures of iron-dependent regulator family members so far. The 2D-IdeR-DNA complex structures confirm the specificity of Ser37 and Pro39 for thymine bases and suggest preferential contacts of Gln43 to cytosine bases of the DNA. In addition, our 2D-IdeR structures reveal a remarkable property of the TEV cleavage sequence remaining after removal of the C-terminal His6. This C-terminal tail promotes crystal contacts by forming a beta-sheet with the corresponding tail of neighboring subunits in two unrelated structures of 2D-IdeR, one with and one without DNA. The contact-promoting properties of this C-terminal TEV cleavage sequence may be beneficial for crystallizing other proteins.
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==About this Structure==
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Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis.,Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE, Holmes RK, Beeson C, Hol WG Biochemistry. 2007 Jan 16;46(2):436-47. PMID:17209554<ref>PMID:17209554</ref>
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2IT0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with NI and ACT as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IT0 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis., Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE, Holmes RK, Beeson C, Hol WG, Biochemistry. 2007 Jan 16;46(2):436-47. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17209554 17209554]
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</div>
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<div class="pdbe-citations 2it0" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
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[[Category: Single protein]]
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[[Category: Beeson C]]
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[[Category: Beeson, C.]]
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[[Category: Chou CJ]]
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[[Category: Chou, C.J.]]
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[[Category: Hol WG]]
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[[Category: Hol, W.G.]]
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[[Category: Holmes RK]]
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[[Category: Holmes, R.K.]]
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[[Category: Rice AE]]
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[[Category: Rice, A.E.]]
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[[Category: Roach C]]
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[[Category: Roach, C.]]
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[[Category: Wisedchaisri G]]
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[[Category: Wisedchaisri, G.]]
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[[Category: Wu M]]
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[[Category: Wu, M.]]
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[[Category: ACT]]
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[[Category: NI]]
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[[Category: dna-binding protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:31:01 2007''
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Current revision

Crystal structure of a two-domain IdeR-DNA complex crystal form II

PDB ID 2it0

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