Structural homology between <i>rbs</i> repressor and ribose binding protein implies functional similarity

Mauzy, Camilla A; Hermodson, Mark A.

doi:10.1002/pro.5560010702

Cited by 33 publications

(26 citation statements)

References 42 publications

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“…The rbsR gene begins at the unusual start codon TTG located 3 bp downstream of the rbsK stop codon. The three additional amino acids from the predicted protein sequence produced with the TTG start codon are highly similar to other repressor sequences (Mauzy & Hermodson, 1992). An in-frame ATG codon is present 13 bp downstream of rbsK.…”

Section: Sequence Of Rbsrmentioning

confidence: 76%

“…By homology to LacI (Mauzy & Hermodson, 1992) the first 60 residues of RbsR form the DNA-binding domain. The highest degree of similarity between the members of this family of repressors is found in this domain, and the most similar region of all spans the first 22 residues of RbsR.…”

Section: Ecorlmentioning

confidence: 99%

“…The degree of similarity is so striking in both the protein sequences ( Fig. 1; Mauzy & Hermodson, 1992) and the operator sequences (Fig. 6) that the question of how specificity is attained must be considered.…”

Section: Ecorlmentioning

confidence: 99%

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Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli

Mauzy

Hermodson

1992

Protein Science

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The DNA sequence encoding the rbs repressor protein, RbsR, has been determined. Amino acid sequence analyses of the product of an rbsR-lac2 fusion and of affinity-purified RbsR demonstrate that translation begins at an unusual codon, TTG, and that the initial amino acid is removed during maturation of the protein. DNA-binding assays indicate that RbsR binds to a region of perfect dyad symmetry spanning the rbs operon transcriptional start site and that the affinity for the rbs operator is reduced by addition of ribose, consistent with ribose being the inducer of the operon. RbsR is a member of a family of homologous repressor proteins having very similar DNA-binding sites and binding to similar operator sequences. [RbsR PIR accession number A41828.1 Keywords: Escherichia coli; repressors; ribose transport and utilization; transcription regulationThe rbs operon of Escherichia coli K12 encodes the highaffinity membrane transport system for ribose (Iida et al., 1984; Lopilato et al., 1984). Three open reading frames at the 5' end of the mRNA, designated rbsD, rbsA, and rbsC , are located in the region shown to be necessary for the membrane transport function (Iida et al., 1984;Lopilato et al., 1984). The coding region for the periplasmic ribose binding protein, rbsB, follows (Groarke et al., 1983), with that for ribokinase, rbsK , completing the set of genes that have been demonstrated to function as a single transcriptional unit (Lopilato et al., 1984).The gene encoding the repressor for the rbs operon, rbsR, was shown to be located downstream from rbsK, and evidence indicated that it is on a separate transcriptional unit from rbs (Lopilato et al ., 1984). During the sequence analysis, we found an open reading frame immediately downstream of rbsK that was clearly homologous to lacland galR . We have now completed the sequence analysis of this open reading frame and have shown that it encodes RbsR, a member of a family of repressor proteins. Functional studies have confirmed that the protein is expressed and binds to DNA sequences upstream of rbsD that conform to the consensus operator sequences for this family of repressors. These studies, together with the earlier genetic analyses (Lopilato et al., 1984), identify and locate the rbsR gene.

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Section: Sequence Of Rbsrmentioning

confidence: 76%

Section: Ecorlmentioning

confidence: 99%

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Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli

Mauzy

Hermodson

1992

Protein Science

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“…2) were the only fully conserved residues in the multiple alignment of the 25 LGF proteins included in our study. Other residues in the H-T-H region ( The functional significance of some of these residues in specific members of the LGF is known and has been discussed [6,7,10,13,17]. For example, in PurR, S 14 (alignment position 22) hydrogen bonds to T17 (alignment position 25) accounting in part for the conservation of these residues.…”

Section: Multiple Alignment Of Lgf Proteinsmentioning

confidence: 99%

“…Tile 3-dimensional structures of both the liganded and the unliganded forms of some of these proteins are known [6][7][8]19,20]. Outside of the regions of the LGF protein sequences depicted in Fig.…”

Section: Sequence Divergence Of the Large C-terminal Ligand-bindingmentioning

confidence: 99%

Phylogenetic, structural and functional analyses of the LacI‐GalR family of bacterial transcription factors

Nguyen

Saier

1995

FEBS Letters

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Phylogenetic tree construction for 25 sequenced members of the LacI-GalR family (LGF) of transcription factors revealed that almost all branches are similar in length, radiating essentially from a single point. This observation suggests that most of these proteins arose by duplication events which occurred at a specific time in evolutionary history, and that further duplication events were rare. Analyses of the multiple alignment of the LGF proteins lead to suggestions regarding structure-function relationships and reveal that the helix-turn-helix DNA-binding motif of LGF proteins is similar in sequence to those of numerous non-homologous DNA-binding proteins.

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Enzymatic protein switches built from paralogous input domains

Tullman

Nicholes

Dumont

et al. 2015

Biotech & Bioengineering

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Protein switches have a variety of potential applications in biotechnology and medicine that motivate efforts to accelerate their development. Switches can be built by the proper fusion of two proteins with the prerequisite input and output functions. However, the exact fusion geometry for switch creation, which typically involves insertion of one protein domain into the other, is difficult to predict. Based on our previous work developing protein switches using periplasmic binding proteins as input domains, we wondered whether there are "hot spots" for insertion of output domains and successful switch creation within this class of proteins. Here we describe directed evolution experiments that identified switches in which TEM-1 beta-lactamase (BLA) is inserted into the class I periplasmic binding proteins ribose binding protein (RBP), glucose binding protein (GBP), and xylose binding protein (XBP). Although some overlap in sites for successful switch insertion could be found among the paralogs, successful switches at these sites required different linkers between the domains and different circular permutations of the BLA protein. Our data suggests that sites for successful switch creation are not easily transferable between paralogs. Furthermore, by comparison to a previous study in which switches were created by inserting a xylanase into XBP, we find no correlation between insertion sites when using two different output domains. We conclude that the switch property likely depends on the precise molecular details of the fusions and cannot be easily predicted from some overall general structural property of the fusion topology.

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Structural homology between rbs repressor and ribose binding protein implies functional similarity

Cited by 33 publications

References 42 publications

Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli

Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli

Phylogenetic, structural and functional analyses of the LacI‐GalR family of bacterial transcription factors

Enzymatic protein switches built from paralogous input domains

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