2isz: Difference between revisions

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{{Seed}}
[[Image:2isz.png|left|200px]]


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==Crystal structure of a two-domain IdeR-DNA complex crystal form I==
The line below this paragraph, containing "STRUCTURE_2isz", creates the "Structure Box" on the page.
<StructureSection load='2isz' size='340' side='right'caption='[[2isz]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2isz]] 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=2ISZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ISZ FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.403&#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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
{{STRUCTURE_2isz|  PDB=2isz  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2isz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isz OCA], [https://pdbe.org/2isz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2isz RCSB], [https://www.ebi.ac.uk/pdbsum/2isz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2isz ProSAT]</span></td></tr>
</table>
== Function ==
[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>
== 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/is/2isz_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2isz ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===Crystal structure of a two-domain IdeR-DNA complex crystal form I===
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>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2isz" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 17209554 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17209554}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2ISZ is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISZ OCA].
 
==Reference==
<ref group="xtra">PMID:17209554</ref><references group="xtra"/>
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Beeson, C.]]
[[Category: Beeson C]]
[[Category: Chou, C J.]]
[[Category: Chou CJ]]
[[Category: Hol, W G.]]
[[Category: Hol WG]]
[[Category: Holmes, R K.]]
[[Category: Holmes RK]]
[[Category: Rice, A E.]]
[[Category: Rice AE]]
[[Category: Roach, C.]]
[[Category: Roach C]]
[[Category: Wisedchaisri, G.]]
[[Category: Wisedchaisri G]]
[[Category: Wu, M.]]
[[Category: Wu M]]
[[Category: Dna-binding protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:54:44 2009''
Retrieved from "https://proteopedia.org/2isz"