1uxd

From Proteopedia

(Difference between revisions)

Revision as of 10:32, 25 December 2014

Fructose repressor DNA-binding domain, NMR, 34 structures

Structural highlights

1uxd is a 1 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1uxc
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[FRUR_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.

Publication Abstract from PubMed

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.

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:9237914^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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
↑ 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, 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
↑ 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
↑ 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
↑ 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
↑ Penin F, Geourjon C, Montserret R, Bockmann A, Lesage A, Yang YS, Bonod-Bidaud C, Cortay JC, Negre D, Cozzone AJ, Deleage G. Three-dimensional structure of the DNA-binding domain of the fructose repressor from Escherichia coli by 1H and 15N NMR. J Mol Biol. 1997 Jul 18;270(3):496-510. PMID:9237914 doi:10.1006/jmbi.1997.1123

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1uxd"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1uxd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UXD FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uxc|1uxc]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uxc|1uxc]]</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uxd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uxd RCSB], [http://www.ebi.ac.uk/pdbsum/1uxd PDBsum]</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=1uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uxd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uxd RCSB], [http://www.ebi.ac.uk/pdbsum/1uxd PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/FRUR_ECOLI FRUR_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:8230205</ref> <ref>PMID:8195118</ref> <ref>PMID:8577250</ref> <ref>PMID:8550429</ref> <ref>PMID:8858581</ref> <ref>PMID:9084760</ref> <ref>PMID:9371462</ref> <ref>PMID:16115199</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 29: / Line 31: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Bockmann, A.]]
+[[Category: Bockmann, A]]
-[[Category: Bonod-Bidaud, C.]]
+[[Category: Bonod-Bidaud, C]]
-[[Category: Cortay, J C.]]
+[[Category: Cortay, J C]]
-[[Category: Cozzone, A J.]]
+[[Category: Cozzone, A J]]
-[[Category: Deleage, G.]]
+[[Category: Deleage, G]]
-[[Category: Geourjon, C.]]
+[[Category: Geourjon, C]]
-[[Category: Lesage, A.]]
+[[Category: Lesage, A]]
-[[Category: Montserret, R.]]
+[[Category: Montserret, R]]
-[[Category: Negre, D.]]
+[[Category: Negre, D]]
-[[Category: Penin, F.]]
+[[Category: Penin, F]]
-[[Category: Yang, Y.]]
+[[Category: Yang, Y]]
 [[Category: Dna-binding protein]]
 [[Category: Fructose repressor]]
 [[Category: Laci family]]
 [[Category: Transcription regulation]]

1uxd

From Proteopedia

Revision as of 10:32, 25 December 2014

Fructose repressor DNA-binding domain, NMR, 34 structures

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox