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| | ==Crystal structure of a two-domain IdeR-DNA complex crystal form II== | | ==Crystal structure of a two-domain IdeR-DNA complex crystal form II== |
| - | <StructureSection load='2it0' size='340' side='right' caption='[[2it0]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='2it0' size='340' side='right'caption='[[2it0]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2it0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IT0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2it0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. 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> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | + | </td></tr><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> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fx7|1fx7]], [[1u8r|1u8r]], [[2isy|2isy]], [[2isz|2isz]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fx7|1fx7]], [[1u8r|1u8r]], [[2isy|2isy]], [[2isz|2isz]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IdeR,dtxR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IdeR,dtxR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=2it0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2it0 OCA], [http://pdbe.org/2it0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2it0 RCSB], [http://www.ebi.ac.uk/pdbsum/2it0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2it0 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=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> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [[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 == | | == 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: Large Structures]] |
| | [[Category: Beeson, C]] | | [[Category: Beeson, C]] |
| | [[Category: Chou, C J]] | | [[Category: Chou, C J]] |
| Structural highlights
Function
[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.[1] [2]
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 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 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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gold B, Rodriguez GM, Marras SA, Pentecost M, Smith I. The Mycobacterium tuberculosis IdeR is a dual functional regulator that controls transcription of genes involved in iron acquisition, iron storage and survival in macrophages. Mol Microbiol. 2001 Nov;42(3):851-65. PMID:11722747
- ↑ Rodriguez GM, Voskuil MI, Gold B, Schoolnik GK, Smith I. ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect Immun. 2002 Jul;70(7):3371-81. PMID:12065475
- ↑ Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE, Holmes RK, Beeson C, Hol WG. Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis. Biochemistry. 2007 Jan 16;46(2):436-47. PMID:17209554 doi:10.1021/bi0609826
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