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| | ==Crystal structure of IcaR, a repressor of the TetR family== | | ==Crystal structure of IcaR, a repressor of the TetR family== |
| - | <StructureSection load='2zcm' size='340' side='right' caption='[[2zcm]], [[Resolution|resolution]] 1.33Å' scene=''> | + | <StructureSection load='2zcm' size='340' side='right'caption='[[2zcm]], [[Resolution|resolution]] 1.33Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zcm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staeq Staeq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZCM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZCM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zcm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis_RP62A Staphylococcus epidermidis RP62A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZCM FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 1.33Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2zcn|2zcn]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IcaR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176279 STAEQ])</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=2zcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zcm OCA], [https://pdbe.org/2zcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zcm RCSB], [https://www.ebi.ac.uk/pdbsum/2zcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zcm 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=2zcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zcm OCA], [http://pdbe.org/2zcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zcm RCSB], [http://www.ebi.ac.uk/pdbsum/2zcm PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ICAR_STAEQ ICAR_STAEQ]] Represses transcription of the icaADBC operon necessary for biofilm production.<ref>PMID:12142410</ref> | + | [https://www.uniprot.org/uniprot/ICAR_STAEQ ICAR_STAEQ] Represses transcription of the icaADBC operon necessary for biofilm production.<ref>PMID:12142410</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zc/2zcm_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zc/2zcm_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Staeq]] | + | [[Category: Large Structures]] |
| - | [[Category: Guo, R T]] | + | [[Category: Staphylococcus epidermidis RP62A]] |
| - | [[Category: Jeng, W Y]] | + | [[Category: Guo RT]] |
| - | [[Category: Ko, T P]] | + | [[Category: Jeng WY]] |
| - | [[Category: Liu, C I]] | + | [[Category: Ko TP]] |
| - | [[Category: Shr, H L]] | + | [[Category: Liu CI]] |
| - | [[Category: Wang, A H.J]] | + | [[Category: Shr HL]] |
| - | [[Category: Biofilm]] | + | [[Category: Wang AHJ]] |
| - | [[Category: Dna-binding]]
| + | |
| - | [[Category: Helix-turn-helix]]
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| - | [[Category: Repressor]]
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| - | [[Category: Tetr family]]
| + | |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transcription regulation]]
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| Structural highlights
Function
ICAR_STAEQ Represses transcription of the icaADBC operon necessary for biofilm production.[1]
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
Expression of the gene cluster icaADBC is necessary for biofilm production in Staphylococcus epidermidis. The ica operon is negatively controlled by the repressor IcaR. Here, the crystal structure of IcaR was determined and the refined structure revealed a homodimer comprising entirely alpha-helices, typical of the tetracycline repressor protein family for gene regulations. The N-terminal domain contains a conserved helix-turn-helix DNA-binding motif with some conformational variations, indicating flexibility in this region. The C-terminal domain shows a complementary surface charge distribution about the dyad axis, ideal for efficient and specific dimer formation. The results of the electrophoretic mobility shift assay and isothermal titration calorimetry suggested that a 28 bp core segment of the ica operator is implicated in the cooperative binding of two IcaR dimers on opposite sides of the duplex DNA. Computer modeling based on the known DNA-complex structure of QacR and site-specific mutagenesis experiments showed that direct protein-DNA interactions are mostly conserved, but with slight variations for recognizing the different sequences. By interfering with the binding of IcaR to DNA, aminoglycoside gentamicin and other antibiotics may activate the icaADBC genes and elicit biofilm production in S. epidermidis, and likely S. aureus, as a defense mechanism.
Crystal structure of IcaR, a repressor of the TetR family implicated in biofilm formation in Staphylococcus epidermidis.,Jeng WY, Ko TP, Liu CI, Guo RT, Liu CL, Shr HL, Wang AH Nucleic Acids Res. 2008 Mar;36(5):1567-77. Epub 2008 Jan 21. PMID:18208836[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Conlon KM, Humphreys H, O'Gara JP. icaR encodes a transcriptional repressor involved in environmental regulation of ica operon expression and biofilm formation in Staphylococcus epidermidis. J Bacteriol. 2002 Aug;184(16):4400-8. PMID:12142410
- ↑ Jeng WY, Ko TP, Liu CI, Guo RT, Liu CL, Shr HL, Wang AH. Crystal structure of IcaR, a repressor of the TetR family implicated in biofilm formation in Staphylococcus epidermidis. Nucleic Acids Res. 2008 Mar;36(5):1567-77. Epub 2008 Jan 21. PMID:18208836 doi:http://dx.doi.org/10.1093/nar/gkm1176
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