A genetic analysis of various functions of the TyrR protein of Escherichia coli

Yang, Jiyeon; Ganesan, Saampras; Sarsero, Joseph P.; Pittard, A. J.

doi:10.1128/jb.175.6.1767-1776.1993

Cited by 61 publications

(92 citation statements)

References 55 publications

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“…1) show a clear cluster in the loop region following P-strand P3 and in the COOH-terminus amino acid region. There is a reported mutation in the equivalent loop for the TyrR Central domain that has effects on the repression function of this protein (Yang et al, 1993) (see below) and, as mentioned below, there is an absolutely conserved cysteine-rich motif that spans the boundary between the Central domain and an interdomain linker observed exclusively in most of the NifA proteins.…”

Section: Analysis Of Family Sequencesmentioning

confidence: 98%

“…Partial overlapping of predicted correlated mutations for both families of proteins lend additional support to the mononucleotide-binding fold assignment. Figure 4 also shows critical residues of the Central domain mapped by mutagenesis experiments (Table 7) (Austin et al, 1991;Weiss et al, 1991Weiss et al, , 1992Yang et al, 1993;Kwok et al, 1995). Red dots indicate residues mutated in different members of the family that impair ATPase activity.…”

Section: The Ef-tu Fold As a Modelmentioning

confidence: 99%

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A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition

1997

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The expression of genes transcribed by the RNA polymerase with the alternative sigma factor os4 ( E d 4 ) is absolutely dependent on activator proteins that bind to enhancer-like sites, located far upstream from the promoter. These unique prokaryotic proteins, known as enhancer-binding proteins (EBP), mediate open promoter complex formation in a reaction dependent on NTP hydrolysis. The best characterized proteins of this family of regulators are NtrC and NifA, which activate genes required for ammonia assimilation and nitrogen fixation, respectively. In a recent IRBM course ("Frontiers of protein structure prediction," IRBM, Pomezia, Italy, 1995; see web site http://www.mrc-cpe.cam.uk/ irbm-course95/), one of us (J.O.) participated in the elaboration of the proposal that the Central domain of the EBPs might adopt the classical mononucleotide-binding fold. This suggestion was based on the results of a new protein fold recognition algorithm (Map) and in the mapping of correlated mutations calculated for the sequence family on the same mononucleotide-binding fold topology. In this work, we present new data that support the previous conclusion. The results from a number of different secondary structure prediction programs suggest that the Central domain could adopt an alp topology. The fold recognition programs ProFIT 0.9, 3D PROFILE combined with secondary structure prediction, and 123D suggest a mononucleotide-binding fold topology for the Central domain amino acid sequence. Finally, and most importantly, three of five reported residue alterations that impair the Central domain ATPase activity of the E d 4 activators are mapped to polypeptide regions that might be playing equivalent roles as those involved in nucleotidebinding in the mononucleotide-binding proteins. Furthermore, the known residue substitutions that alter the function of the Eos4 activators, leaving intact the Central domain ATPase activity, are mapped on a region proposed to play an equivalent role as the effector region of the GTPase superfamily.

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Section: Analysis Of Family Sequencesmentioning

confidence: 98%

Section: The Ef-tu Fold As a Modelmentioning

confidence: 99%

A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition

1997

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“…5B). 26 It seems, therefore, that TyrR activity is absent in ΔrybA under peroxide stress. To test if TyrR is required for the activity of RybA we constructed a double mutant deficient in both TyrR and RybA by knockout of rybA in JP 8042 cells.…”

Section: Discussionmentioning

confidence: 99%

The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress inE. coli

Gerstle¹,

Klätschke²,

Hahn³

et al. 2012

RNA Biology

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“…ATP has a major effect on the unfolding of the central domain of H. influenzae TyrR (35). Mutations in the ATP-binding motif of E. coli TyrR produce a protein that is unable to repress tyrosinerepressible genes and is defective in tyrosine-induced hexamerization (36). The conformational change produced by ATP presumably increases the affinity of the aromatic amino acid binding site in the central domain.…”

Section: Tyrr-(188 -467) Self-associates To a Hexamer In Response To mentioning

confidence: 99%

The Central Domain of Escherichia coli TyrR Is Responsible for Hexamerization Associated with Tyrosine-mediated Repression of Gene Expression

Dixon

Pau

Howlett

et al. 2002

Journal of Biological Chemistry

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TyrR from Escherichia coli regulates the expression of genes for aromatic amino acid uptake and biosynthesis. Its central ATP-hydrolyzing domain is similar to conserved domains of bacterial regulatory proteins that interact with RNA polymerase holoenzyme associated with the alternative sigma factor, 54 . It is also related to the common module of the AAA؉ superfamily of proteins that is involved in a wide range of cellular activities. We expressed and purified two TyrR central domain polypeptides. The fragment comprising residues 188 -467, called TyrR-(188 -467), was soluble and stable, in contrast to that corresponding to the conserved core from residues 193 to 433. TyrR-(188 -467) bound ATP and rhodamine-ATP with association constants 2-to 5-fold lower than TyrR and hydrolyzed ATP at five times the rate of TyrR. In contrast to TyrR, which is predominantly dimeric at protein concentrations less than 10 M in the absence of ligands, or in the presence of ATP or tyrosine alone, TyrR-(188 -467) is a monomer, even at high protein concentrations. Tyrosine in the presence of ATP or ATP␥S promotes the oligomerization of TyrR-(188 -467) to a hexamer. Tyrosine-dependent repression of gene transcription by TyrR therefore depends on ligand binding and hexamerization determinants located in the central domain polypeptide TyrR-(188 -467).

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A genetic analysis of various functions of the TyrR protein of Escherichia coli

Cited by 61 publications

References 55 publications

A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition

A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition

The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress inE. coli

The Central Domain of Escherichia coli TyrR Is Responsible for Hexamerization Associated with Tyrosine-mediated Repression of Gene Expression

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