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MeSH Review

Helix-Turn-Helix Motifs

 
 
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Disease relevance of Helix-Turn-Helix Motifs

 

High impact information on Helix-Turn-Helix Motifs

  • The structure also reveals a helix-turn-helix motif containing an arginine-rich alpha helix that is required for binding to SRP RNA and is implicated in forming the core of an extended RNA binding surface [4].
  • Rather, a large hydrophobic surface patch is found in a novel helix-turn-helix motif, which is characteristic of all group II chaperonins including the eukaryotic TRiC/CCT complex [5].
  • We investigated the nature of homeodomain-DNA interactions by making a series of mutations in the helix-turn-helix motif of the Drosophila homeodomain protein Paired (Prd) [6].
  • The structure provides the first three-dimensional view of a member of the growing IRF family, revealing a new helix-turn-helix motif that latches onto DNA through three of the five conserved tryptophans [7].
  • Four of amino acids that directly interact with the DNA are highly conserved: two arginines from the recognition helix lying in the major groove, one lysine from the 'wing' that binds upstream of the core GGAA sequence, and another lysine, from the 'turn' of the 'helix-turn-helix' motif, which binds downstream and on the opposite strand [8].
 

Chemical compound and disease context of Helix-Turn-Helix Motifs

 

Biological context of Helix-Turn-Helix Motifs

 

Associations of Helix-Turn-Helix Motifs with chemical compounds

 

Gene context of Helix-Turn-Helix Motifs

  • We report a systematic mutational analysis of the helix-turn-helix motif (HTH) of the fushi tarazu (ftz) homeo domain (HD) of Drosophila [21].
  • Changes in the backbone amide proton and nitrogen chemical shifts upon DNA binding have enabled us to experimentally define a DNA-binding surface on the core N-terminal domain of Mbp1 that is associated with a putative winged helix-turn-helix motif [22].
  • Secondary structure analysis of the FSHR R265-S296 primary sequence, which has little homology to LHR, predicted a helix-turn-helix motif [23].
  • The gntR product is 331 amino acids long, with a helix-turn-helix motif typical of a regulatory protein [24].
  • The mutation in strain PAT-2 is the deletion of G at nucleotide 1342 in the patB gene, resulting in the loss of a 62-amino-acid fragment from the C terminus of the PatB protein, including the helix-turn-helix motif [25].
 

Analytical, diagnostic and therapeutic context of Helix-Turn-Helix Motifs

  • Site-directed mutagenesis of the PerA protein suggests that, like VirF, it may use both of its carboxy-terminal helix-turn-helix motifs for DNA interaction, and may also make direct contacts with RNA polymerase [26].
  • On the basis of the protein sequence alignment, a DNA-binding alpha helix-beta turn-alpha helix (HTH) motif was identified in the N-terminal region (residues 18-37) of the repressor as well as in the polypeptide of ORF4 (residues 22-41) [27].
  • The 1,011-base-pair rafR gene encodes a 336-amino-acid polypeptide containing an N-terminal helix-turn-helix motif. rafO, as defined by in vivo titration of raf repressor, consists of two nearly identical 18-base-pair palindromes that flank the -35 box of the raf promoter [28].
  • Sequence analysis of SoxR suggested a helix-turn-helix (HTH) motif at position 87-108 and uncovered an invariant Cys-80 and a cysteine residue at the C-terminus [29].

References

  1. Conversion of a helix-turn-helix motif sequence-specific DNA binding protein into a site-specific DNA cleavage agent. Ebright, R.H., Ebright, Y.W., Pendergrast, P.S., Gunasekera, A. Proc. Natl. Acad. Sci. U.S.A. (1990) [Pubmed]
  2. Phenyl-azide-mediated photocrosslinking analysis of Cro-DNA interaction. Chen, Y., Ebright, R.H. J. Mol. Biol. (1993) [Pubmed]
  3. Trifluoroethanol stabilizes a helix-turn-helix motif in equine infectious-anemia-virus trans-activator protein. Sticht, H., Willbold, D., Ejchart, A., Rosin-Arbesfeld, R., Yaniv, A., Gazit, A., Rösch, P. Eur. J. Biochem. (1994) [Pubmed]
  4. Crystal structure of the signal sequence binding subunit of the signal recognition particle. Keenan, R.J., Freymann, D.M., Walter, P., Stroud, R.M. Cell (1998) [Pubmed]
  5. Structure of the substrate binding domain of the thermosome, an archaeal group II chaperonin. Klumpp, M., Baumeister, W., Essen, L.O. Cell (1997) [Pubmed]
  6. A single amino acid can determine the DNA binding specificity of homeodomain proteins. Treisman, J., Gönczy, P., Vashishtha, M., Harris, E., Desplan, C. Cell (1989) [Pubmed]
  7. Structure of IRF-1 with bound DNA reveals determinants of interferon regulation. Escalante, C.R., Yie, J., Thanos, D., Aggarwal, A.K. Nature (1998) [Pubmed]
  8. A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. Kodandapani, R., Pio, F., Ni, C.Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R.A., Ely, K.R. Nature (1996) [Pubmed]
  9. Structural analysis of the purine repressor, an Escherichia coli DNA-binding protein. Schumacher, M.A., Macdonald, J.R., Björkman, J., Mowbray, S.L., Brennan, R.G. J. Biol. Chem. (1993) [Pubmed]
  10. E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Lawson, C.L., Benoff, B., Berger, T., Berman, H.M., Carey, J. Structure (Camb.) (2004) [Pubmed]
  11. A core promoter element downstream of the TATA box that is recognized by TFIIB. Deng, W., Roberts, S.G. Genes Dev. (2005) [Pubmed]
  12. Analysis of a carbapenem-hydrolyzing class A beta-lactamase from Enterobacter cloacae and of its LysR-type regulatory protein. Naas, T., Nordmann, P. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  13. The RNA binding domain of Jerky consists of tandemly arranged helix-turn-helix/homeodomain-like motifs and binds specific sets of mRNAs. Liu, W., Seto, J., Sibille, E., Toth, M. Mol. Cell. Biol. (2003) [Pubmed]
  14. MSH4 acts in conjunction with MLH1 during mammalian meiosis. Santucci-Darmanin, S., Walpita, D., Lespinasse, F., Desnuelle, C., Ashley, T., Paquis-Flucklinger, V. FASEB J. (2000) [Pubmed]
  15. Mutations in the helix-turn-helix motif of the Escherichia coli UvrA protein eliminate its specificity for UV-damaged DNA. Wang, J., Grossman, L. J. Biol. Chem. (1993) [Pubmed]
  16. The three-dimensional structure of trp repressor. Schevitz, R.W., Otwinowski, Z., Joachimiak, A., Lawson, C.L., Sigler, P.B. Nature (1985) [Pubmed]
  17. Three-dimensional crystal structures of Escherichia coli met repressor with and without corepressor. Rafferty, J.B., Somers, W.S., Saint-Girons, I., Phillips, S.E. Nature (1989) [Pubmed]
  18. A chemically synthesized Antennapedia homeo domain binds to a specific DNA sequence. Mihara, H., Kaiser, E.T. Science (1988) [Pubmed]
  19. Determination of the orientation of a DNA binding motif in a protein-DNA complex by photocrosslinking. Pendergrast, P.S., Chen, Y., Ebright, Y.W., Ebright, R.H. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  20. Molecular cloning of the high affinity calcium-binding protein (calreticulin) of skeletal muscle sarcoplasmic reticulum. Fliegel, L., Burns, K., MacLennan, D.H., Reithmeier, R.A., Michalak, M. J. Biol. Chem. (1989) [Pubmed]
  21. In vivo analysis of the helix-turn-helix motif of the fushi tarazu homeo domain of Drosophila melanogaster. Furukubo-Tokunaga, K., Müller, M., Affolter, M., Pick, L., Kloter, U., Gehring, W.J. Genes Dev. (1992) [Pubmed]
  22. Characterization of the DNA-binding domains from the yeast cell-cycle transcription factors Mbp1 and Swi4. Taylor, I.A., McIntosh, P.B., Pala, P., Treiber, M.K., Howell, S., Lane, A.N., Smerdon, S.J. Biochemistry (2000) [Pubmed]
  23. Accessibility of rat and human follitropin receptor primary sequence (R265-S296) in situ. Liu, X., DePasquale, J.A., Griswold, M.D., Dias, J.A. Endocrinology (1994) [Pubmed]
  24. Cloning and molecular genetic characterization of the Escherichia coli gntR, gntK, and gntU genes of GntI, the main system for gluconate metabolism. Tong, S., Porco, A., Isturiz, T., Conway, T. J. Bacteriol. (1996) [Pubmed]
  25. The patB gene product, required for growth of the cyanobacterium Anabaena sp. strain PCC 7120 under nitrogen-limiting conditions, contains ferredoxin and helix-turn-helix domains. Liang, J., Scappino, L., Haselkorn, R. J. Bacteriol. (1993) [Pubmed]
  26. Direct and indirect transcriptional activation of virulence genes by an AraC-like protein, PerA from enteropathogenic Escherichia coli. Porter, M.E., Mitchell, P., Roe, A.J., Free, A., Smith, D.G., Gally, D.L. Mol. Microbiol. (2004) [Pubmed]
  27. Interaction of a putative transcriptional regulatory protein and the thermo-inducible cts-52 mutant repressor in the Bacillus subtilis phage phi105 genome. Chan, A.Y., Lim, B.L. J. Mol. Biol. (2003) [Pubmed]
  28. Regulatory elements of the raffinose operon: nucleotide sequences of operator and repressor genes. Aslanidis, C., Schmitt, R. J. Bacteriol. (1990) [Pubmed]
  29. SoxRS-mediated regulation of chemotrophic sulfur oxidation in Paracoccus pantotrophus. Rother, D., Orawski, G., Bardischewsky, F., Friedrich, C.G. Microbiology (Reading, Engl.) (2005) [Pubmed]
 
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