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| - | [[Image:1uxd.jpg|left|200px]]<br /><applet load="1uxd" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1uxd" /> | |
| - | '''FRUCTOSE REPRESSOR DNA-BINDING DOMAIN, NMR, 34 STRUCTURES'''<br /> | |
| | | | |
| - | ==Overview== | + | ==Fructose repressor DNA-binding domain, NMR, 34 structures== |
| - | FruR is an Escherichia coli transcriptional regulator that belongs to the, LacI DNA-binding protein family. By using 1H and 15N NMR spectroscopy, we, have determined the three-dimensional solution structure of the FruR, N-terminal DNA-binding domain consisting of 57 amino acid residues. A, total of 809 NMR-derived distances and 54 dihedral angle constraints have, been used for molecular modelling with the X-PLOR program. The resulting, set of calculated structures presents an average root-mean-square, deviation of 0.37 A at the main-chain level for the first 47 residues., This highly defined N-terminal part of the structure reveals a similar, topology for the three alpha-helices when compared to the 3D structures of, LacI and PurR counterparts. The most striking difference lies in the, connection between helix II and helix III, in which three additional, residues are present in FruR. This connecting segment is well structured, and contains a type III turn. Apart from hydrophobic interactions of, non-polar residues with the core of the domain, this connecting segment is, stabilised by several hydrogen bonds and by the aromatic ring stacking, between Tyr19 of helix II and Tyr28 of the turn. The region containing the, putative "hinge helix" (helix IV), that has been described in PurR-DNA, complex to make specific base contacts in the minor groove of DNA, is, unfolded. Examination of hydrogen bonds highlights the importance of, homologous residues that seem to be conserved for their ability to fulfill, helix N and C-capping roles in the LacI repressor family.
| + | <StructureSection load='1uxd' size='340' side='right'caption='[[1uxd]]' scene=''> |
| - | | + | == Structural highlights == |
| - | ==About this Structure== | + | <table><tr><td colspan='2'>[[1uxd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UXD FirstGlance]. <br> |
| - | 1UXD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Known structural/functional Site: <scene name='pdbsite=HTH:Hth_laci+Family'>HTH</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UXD OCA].
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uxd OCA], [https://pdbe.org/1uxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uxd RCSB], [https://www.ebi.ac.uk/pdbsum/1uxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uxd ProSAT]</span></td></tr> |
| - | ==Reference== | + | </table> |
| - | Three-dimensional structure of the DNA-binding domain of the fructose repressor from Escherichia coli by 1H and 15N NMR., Penin F, Geourjon C, Montserret R, Bockmann A, Lesage A, Yang YS, Bonod-Bidaud C, Cortay JC, Negre D, Cozzone AJ, Deleage G, J Mol Biol. 1997 Jul 18;270(3):496-510. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9237914 9237914]
| + | == Function == |
| - | [[Category: Escherichia coli]] | + | [https://www.uniprot.org/uniprot/CRA_ECOLI CRA_ECOLI] Global transcriptional regulator, which plays an important role in the regulation of carbon metabolism. Activates transcription of genes encoding biosynthetic and oxidative enzymes (involved in Krebs cycle, glyoxylate shunt and gluconeogenesis, such as ppsA and fbp). Represses genes involved in sugar catabolism, such as fruB, pfkA, pykF and adhE. Binds asymmetrically to the two half-sites of its operator.<ref>PMID:16115199</ref> <ref>PMID:8195118</ref> <ref>PMID:8230205</ref> <ref>PMID:8550429</ref> <ref>PMID:8577250</ref> <ref>PMID:8858581</ref> <ref>PMID:9084760</ref> <ref>PMID:9371462</ref> |
| - | [[Category: Single protein]] | + | == Evolutionary Conservation == |
| - | [[Category: Bockmann, A.]] | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | [[Category: Bonod-Bidaud, C.]] | + | Check<jmol> |
| - | [[Category: Cortay, J.C.]] | + | <jmolCheckbox> |
| - | [[Category: Cozzone, A.J.]] | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ux/1uxd_consurf.spt"</scriptWhenChecked> |
| - | [[Category: Deleage, G.]] | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | [[Category: Geourjon, C.]] | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | [[Category: Lesage, A.]] | + | </jmolCheckbox> |
| - | [[Category: Montserret, R.]] | + | </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=1uxd ConSurf]. |
| - | [[Category: Negre, D.]] | + | <div style="clear:both"></div> |
| - | [[Category: Penin, F.]] | + | == References == |
| - | [[Category: Yang, Y.]] | + | <references/> |
| - | [[Category: dna-binding protein]]
| + | __TOC__ |
| - | [[Category: fructose repressor]]
| + | </StructureSection> |
| - | [[Category: laci family]]
| + | [[Category: Escherichia coli K-12]] |
| - | [[Category: transcription regulation]]
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Bockmann A]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:09:04 2008''
| + | [[Category: Bonod-Bidaud C]] |
| | + | [[Category: Cortay JC]] |
| | + | [[Category: Cozzone AJ]] |
| | + | [[Category: Deleage G]] |
| | + | [[Category: Geourjon C]] |
| | + | [[Category: Lesage A]] |
| | + | [[Category: Montserret R]] |
| | + | [[Category: Negre D]] |
| | + | [[Category: Penin F]] |
| | + | [[Category: Yang Y]] |
| Structural highlights
Function
CRA_ECOLI Global transcriptional regulator, which plays an important role in the regulation of carbon metabolism. Activates transcription of genes encoding biosynthetic and oxidative enzymes (involved in Krebs cycle, glyoxylate shunt and gluconeogenesis, such as ppsA and fbp). Represses genes involved in sugar catabolism, such as fruB, pfkA, pykF and adhE. Binds asymmetrically to the two half-sites of its operator.[1] [2] [3] [4] [5] [6] [7] [8]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
References
- ↑ Shimada T, Fujita N, Maeda M, Ishihama A. Systematic search for the Cra-binding promoters using genomic SELEX system. Genes Cells. 2005 Sep;10(9):907-18. PMID:16115199 doi:http://dx.doi.org/10.1111/j.1365-2443.2005.00888.x
- ↑ Cortay JC, Negre D, Scarabel M, Ramseier TM, Vartak NB, Reizer J, Saier MH Jr, Cozzone AJ. In vitro asymmetric binding of the pleiotropic regulatory protein, FruR, to the ace operator controlling glyoxylate shunt enzyme synthesis. J Biol Chem. 1994 May 27;269(21):14885-91. PMID:8195118
- ↑ Ramseier TM, Negre D, Cortay JC, Scarabel M, Cozzone AJ, Saier MH Jr. In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium. J Mol Biol. 1993 Nov 5;234(1):28-44. PMID:8230205 doi:http://dx.doi.org/10.1006/jmbi.1993.1561
- ↑ Bledig SA, Ramseier TM, Saier MH Jr. Frur mediates catabolite activation of pyruvate kinase (pykF) gene expression in Escherichia coli. J Bacteriol. 1996 Jan;178(1):280-3. PMID:8550429
- ↑ Ramseier TM, Bledig S, Michotey V, Feghali R, Saier MH Jr. The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli. Mol Microbiol. 1995 Jun;16(6):1157-69. PMID:8577250
- ↑ Negre D, Bonod-Bidaud C, Geourjon C, Deleage G, Cozzone AJ, Cortay JC. Definition of a consensus DNA-binding site for the Escherichia coli pleiotropic regulatory protein, FruR. Mol Microbiol. 1996 Jul;21(2):257-66. PMID:8858581
- ↑ Ramseier TM. Cra and the control of carbon flux via metabolic pathways. Res Microbiol. 1996 Jul-Sep;147(6-7):489-93. PMID:9084760
- ↑ Mikulskis A, Aristarkhov A, Lin EC. Regulation of expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by catabolite repressor activator protein Cra. J Bacteriol. 1997 Nov;179(22):7129-34. PMID:9371462
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