Protein – DNA interactions: the story so far and a new method for prediction

Jones, Susan R.; Thornton, Janet M.

doi:10.1002/cfg.303

Cited by 8 publications

(2 citation statements)

References 20 publications

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“…Through interaction between the second helix of the HTH motif (i.e. the recognition helix) and the DNA major groove, the sequence information is accessible for the protein [32,52,53]. Recently, proteins with minor groove‐binding HTH motifs have been identified.…”

Section: Discussionmentioning

confidence: 99%

Structure of FocB – a member of a family of transcription factors regulating fimbrial adhesin expression in uropathogenic Escherichia coli

et al. 2010

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In uropathogenic Escherichia coli, UPEC, different types of fimbriae are expressed to mediate interactions with host tissue. FocB belongs to the PapB family of transcription factors involved in the regulation of fimbriae gene clusters. Recent findings suggest that members from this family of proteins may form homomeric or heteromeric complexes and exert both positive and negative effects on the transcription of fimbriae genes. To elucidate the detailed function of FocB, we have determined its crystal structure at 1.4 Å resolution. FocB is an all α‐helical protein with a helix‐turn‐helix motif. Interestingly, conserved residues important for DNA‐binding are located not in the postulated recognition helix of the motif, but in the preceding helix. Results from protein–DNA‐binding studies suggest that FocB interacts with the minor groove of its cognate DNA target, which is indicative of a DNA interaction that is unusual for this motif. FocB crystallizes in the form of dimers. Packing interactions in the crystals give two plausible dimerization interfaces. Conserved residues, known to be important for protein oligomerization, are present at both interfaces, suggesting that both sites could play a role in a functional FocB protein. Structured digital abstract http://mint.bio.uniroma2.it/mint/search/interaction.do?interactionAc=MINT-7901626: focB (uniprotkb:http://www.uniprot.org/uniprot/Q93K76) and focB (uniprotkb:http://www.uniprot.org/uniprot/Q93K76) bind (http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0407) by x‐ray crystallography (http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0114)

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Section: Discussionmentioning

confidence: 99%

Structure of FocB – a member of a family of transcription factors regulating fimbrial adhesin expression in uropathogenic Escherichia coli

et al. 2010

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“…DNA-binding proteins play a pivotal role in the biology of the cell, being responsible for the transfer of biological information from genes to proteins, and have been estimated to constitute ∼6–7% of all proteins expressed by eukaryotic genomes (1,2). A large number of DNA-binding proteins and protein–DNA complexes are deposited in the Protein Data Bank (PDB) (3) and in the Nucleic Acid Database (4).…”

Section: Introductionmentioning

confidence: 99%

Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information

Pellegrini-Calace

2005

Nucleic Acids Research

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In this work, we analyse the potential for using structural knowledge to improve the detection of the DNA-binding helix–turn–helix (HTH) motif from sequence. Starting from a set of DNA-binding protein structures that include a functional HTH motif and have no apparent sequence similarity to each other, two different libraries of hidden Markov models (HMMs) were built. One library included sequence models of whole DNA-binding domains, which incorporate the HTH motif, the second library included shorter models of ‘partial’ domains, representing only the fraction of the domain that corresponds to the functionally relevant HTH motif itself. The libraries were scanned against a dataset of protein sequences, some containing the HTH motifs, others not. HMM predictions were compared with the results obtained from a previously published structure-based method and subsequently combined with it. The combined method proved more effective than either of the single-featured approaches, showing that information carried by motif sequences and motif structures are to some extent complementary and can successfully be used together for the detection of DNA-binding HTHs in proteins of unknown function.

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Current awareness on comparative and functional genomics

2004

Comp Funct Genom

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Protein – DNA interactions: the story so far and a new method for prediction

Cited by 8 publications

References 20 publications

Structure of FocB – a member of a family of transcription factors regulating fimbrial adhesin expression in uropathogenic Escherichia coli

Structure of FocB – a member of a family of transcription factors regulating fimbrial adhesin expression in uropathogenic Escherichia coli

Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information

Current awareness on comparative and functional genomics

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