The phosphorylated form of the enhancer-binding protein NTRC has an ATPase activity that is essential for activation of transcription

Weiss, David S.; Batut, Jacques; Klose, Karl E.; Keener, John; Kustu, Sydney

doi:10.1016/0092-8674(91)90579-n

Cited by 316 publications

(374 citation statements)

References 43 publications

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“…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%

“…The isolated Central domain retains the ability to promote open-complex formation and, as is true for the complete protein, it requires nucleoside triphosphates for this process (Lee et al, 1993;Berger et al, 1994). A putative ATP-binding signature, the Walker A motif (Walker et al, 1982), has been identified in the Central domain of all the EBP, and it has been shown to be critical for activity (Weiss et al, 1991;. The COOH-terminal domain is less conserved and is variable in length.…”

mentioning

confidence: 99%

“…The loop connecting a-helix F @-strand P6 in EF-Tu) to a-helix G in region C7, presents several invariant residues. Amino acid replacements in this loop produce NtrC "repressor" variants (Weiss et al, 1991(Weiss et al, , 1992. Thus, it is possible that this loop is playing the same role in nucleotide binding as the equivalent region in EF-Tu.…”

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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: The Ef-tu Fold As a Modelmentioning

confidence: 99%

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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 activator converts the closed promoter complex to an open complex that is transcriptionally competent (Sasse-Dwight and Gralla, 1988;Morett and Buck, 1989;Popham et al, 1989;Lee et al, 1993;Lee et al, 1994;Perez-Martin and de Lorenzo, 1996b). To catalyse this isomerization, the activator must hydrolyse ATP (Weiss et al, 1991;Lee et al, 1993;Lee et al, 1994;Perez-Martin and de Lorenzo, 1996b) and make productive contact with 54 -holoenzyme through a DNA loop (Buck et al, 1987;Su et al, 1990;Wedel et al, 1990). Interactions between the activator and 54 -holoenzyme are transient, and sites involved in proteinprotein interaction have not been identified in these proteins.…”

Section: Introductionmentioning

confidence: 99%

A conserved region in the σ⁵⁴‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

Wang

Lee

Brewer

et al. 1997

Molecular Microbiology

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SummaryRhizobium melioti DctD activates transcription from the dctA promoter by catalysing the isomerization of closed complexes between 54 -RNA polymerase holoenzyme and the promoter to open complexes. DctD must make productive contact with 54 -holoenzyme and hydrolyse ATP to catalyse this isomerization. To define further the activation process, we sought to isolate mutants of DctD that had reduced affinities for 54 -holoenzyme. Mutagenesis was confined to the well-conserved C3 region of the protein, which is required for coupling ATP hydrolysis to open complex formation in 54 -dependent activators. Mutant forms of DctD that failed to activate transcription and had substitutions in the C-terminal half of the C3 region were efficiently cross-linked to 54 and the ␤-subunit of RNA polymerase, suggesting that they bound normally to 54 -holoenzyme. In contrast, some mutant forms of DctD with amino acid substitutions in the N-terminal half of the C3 region had reduced affinities for 54 and the ␤-subunit in the cross-linking assay. These data suggest that the N-terminal half of the C3 region of DctD contains a site that may contact 54-holoenzyme during open complex formation.

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“…The lysine residue in this motif is the only amino acid within the loop that is thought to directly contact bound Mg.ATP. Mutation of this residue generally abolishes the ATPase activity and the functionality of the protein (Liu and Summers 1988;Weiss et al 1991;Carrera et al 1993).…”

Section: Introductionmentioning

confidence: 99%

The Evolution of the Conserved ATPase Domain (CAD): Reconstructing the History of an Ancient Protein Module

Swaffield

Purugganan

1997

J Mol Evol

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Abstract. The AAA proteins (ATPases Associated with a variety of cellular Activities) are found in eubacterial, archaebacterial, and eukaryotic species and participate in a large number of cellular processes, including protein degradation, vesicle fusion, cell cycle control, and cellular secretory processes. The AAA proteins are characterized by the presence of a 230 to 250-amino acid ATPase domain referred to as the Conserved ATPase Domain or CAD. Phylogenetic analysis of 133 CAD sequences from 38 species reveal that AAA CADs are organized into discrete groups that are related not only in structure but in cellular function. Evolutionary analyses also indicate that the CAD was present in the last common ancestor of eubacteria, archaebacteria, and eukaryotes. The eubacterial CADs are found in metalloproteases, while CAD-containing proteins in the archaebacterial and eukaryotic lineages appear to have diversified by a series of gene duplication events that lead to the establishment of different functional AAA proteins, including proteasomal regulatory, NSF/Sec, and Pas proteins. The phylogeny of the CADs provides the basis for establishing the patterns of evolutionary change that characterize the AAA proteins.

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The phosphorylated form of the enhancer-binding protein NTRC has an ATPase activity that is essential for activation of transcription

Cited by 316 publications

References 43 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

A conserved region in the σ⁵⁴‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

The Evolution of the Conserved ATPase Domain (CAD): Reconstructing the History of an Ancient Protein Module

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The phosphorylated form of the enhancer-binding protein NTRC has an ATPase activity that is essential for activation of transcription

Cited by 316 publications

References 43 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

A conserved region in the σ54‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

The Evolution of the Conserved ATPase Domain (CAD): Reconstructing the History of an Ancient Protein Module

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A conserved region in the σ⁵⁴‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation