Classification of multi‐helical DNA‐binding domains and application to predict the DBD structures of σ factor, LysR, OmpR/PhoB, CENP‐B, Rap1, and XylS/Ada/AraC

@article{Suzuki1995ClassificationOM,
  title={Classification of multi‐helical DNA‐binding domains and application to predict the DBD structures of $\sigma$ factor, LysR, OmpR/PhoB, CENP‐B, Rap1, and XylS/Ada/AraC},
  author={M. Suzuki and Steven E. Brenner},
  journal={FEBS Letters},
  year={1995},
  volume={372}
}
Solution structure of the DNA-binding domain and model for the complex of multifunctiona hexameric arginine represser with DNA
The structure of the monomeric DNA-binding domain of the Escherichia coli arginine represser, ArgR, determined by NMR spectroscope shows structural homology to the winged helix-turn-helix (wHTH)
Comparison of modes of DNA-binding and bending by archaeal transcription factors, Phr, TrmB, GvpE, GvpD, NrpR, Lrs14 and MDR1
TLDR
Characteristics common with known FFRPs are found for all the transcription factors analyzed, consistently with my earlier arguments.
Solution structure of the DNA binding domain from Dead ringer, a sequence‐specific AT‐rich interaction domain (ARID)
TLDR
The solution structure of the Dead ringer ARID (residues Gly262–Gly398) was determined using NMR spectroscopy and suggests that all ARID‐containing proteins contact DNA through the HTH and hairpin structures, but only extended‐ARID proteins supplement this binding surface with a terminal helix.
The DNA-binding domain of feast/famine regulatory protein, FFRP.
Using genomic sequences, gene Bs0711124 of the eubacterium Bacillus subtilis and other archaeal genes including lrs14 of Sulfolobus solfataricus have been identified as coding the N-terminal half of
The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription.
TLDR
This paper describes two forms of the archaeal FFRP FL11 (pot0434017), both assembled from dimers, and proposes a possible mechanism for regulating a number of genes by varying assembly forms and by combining different FFRPs into these assemblies, responding to environmental changes.
Identification of activating region (AR) of Escherichia coli LysR‐type transcription factor CysB and CysB contact site on RNA polymerase alpha subunit at the cysP promoter
TLDR
It is proposed that CysB residues Y27, T28 and S29, lying in this turn region, comprise an ‘activating region’ (AR) that is crucial for positive control of the cysP promoter, but not for DNA binding and inducer response activities of Cys B.
A helix–turn–helix structure unit in human centromere protein B (CENP‐B)
TLDR
The results suggest that CENP‐B DBD RP1 interacts with one of the essential regions of the CENp‐B box DNA, mainly at the N‐terminal basic region, the N-terminal portion of helix 2 and helix 3.
DNA-binding proteins and evolution of transcription regulation in the archaea.
TLDR
It is shown that all archaea encode a large number of proteins containing the helix-turn-helix DNA-binding domains whose sequences are much more similar to bacterial HTH domains than to eukaryotic ones, such as the PAIRED, POU and homeodomains.
Structure and function of the feast/famine regulatory proteins, FFRPs
TLDR
Global regulation by FFRPs can be the prototype of highly differentiated transcription regulatory systems found in organisms nowadays.
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TLDR
It is predicted that the LysR DBD has three α -helices and three β-strands, and that the third α-helix binds to DNA.
Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy.
TLDR
The topology of the LexA DNA binding domain is found to be the same as for the DNA binding domains of the catabolic activator protein, human histone 5, the HNF‐3/fork head protein and the Kluyveromyces heat shock transcription factor.
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TLDR
A possible structure and possible DNA-binding mode of transcription factors in the PhoB/OmpR family are discussed and the amino acid sequences of the DNA- binding domains of factors in this family strongly resemble that of H5.
Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DMA-binding domain bound to its DNA target
TLDR
The dominant transcriptional regulator of the papiIlomaviruses, E2, binds to its specific DNA target through a previously unobserved dimeric ant i para I lei β-barrel through an 'interwoven' network of interactions.
Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices.
The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A
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