DNA recognition by β‐sheets

Tateno, Masaru; Yamasaki, Kazuhiko; Amano, Naoki; Kakinuma, Jun; Koike, Hideaki; Allen, Mark D.; Suzuki, Masashi

doi:10.1002/(sici)1097-0282(1997)44:4<335::aid-bip3>3.3.co;2-i

Cited by 11 publications

(12 citation statements)

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“…The amino termini of the RHH DNA-binding proteins Arc and Mnt are responsible for operator recognition and binding, forming a unique DNA-binding domain (22). The DNA-binding domains of the dimeric protein Arc (53 residues, monomer) and the tetrameric protein Mnt (82 residues, monomer) are similar in structure and assume the shape of an orthogonal bundle (37). The orthogonal bundle is comprised of a beta-strand, which contacts DNA, followed by two alpha helices that form a coiled coil and comprise a dimerization domain (6).…”

Section: Vol 188 2006 Role Of Algz (Amrz) In Twitching Motility 135mentioning

confidence: 99%

The Pseudomonas aeruginosa Ribbon-Helix-Helix DNA-Binding Protein AlgZ (AmrZ) Controls Twitching Motility and Biogenesis of Type IV Pili

et al. 2006

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Pseudomonas aeruginosa is an opportunistic pathogen that is commonly found in water and soil. In order to colonize surfaces with low water content, P. aeruginosa utilizes a flagellum-independent form of locomotion called twitching motility, which is dependent upon the extension and retraction of type IV pili. This study demonstrates that AlgZ, previously identified as a DNA-binding protein absolutely required for transcription of the alginate biosynthetic operon, is required for twitching motility. AlgZ may be required for the biogenesis or function of type IV pili in twitching motility. Transmission electron microscopy analysis of an algZ deletion in nonmucoid PAO1 failed to detect surface pili. To examine expression and localization of PilA (the major pilin subunit), whole-cell extracts and cell surface pilin preparations were analyzed by Western blotting. While the PilA levels present in whole-cell extracts were similar for wild-type P. aeruginosa and P. aeruginosa with the algZ deletion, the amount of PilA on the surface of the cells was drastically reduced in the algZ mutant. Analysis of algZ and algD mutants indicates that the DNA-binding activity of AlgZ is essential for the regulation of twitching motility and that this is independent of the role of AlgZ in alginate expression. These data show that AlgZ DNA-binding activity is required for twitching motility independently of its role in alginate production and that this involves the surface localization of type IV pili. Given this new role in twitching motility, we propose that algZ (PA3385) be designated amrZ (alginate and motility regulator Z).

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Section: Vol 188 2006 Role Of Algz (Amrz) In Twitching Motility 135mentioning

confidence: 99%

The Pseudomonas aeruginosa Ribbon-Helix-Helix DNA-Binding Protein AlgZ (AmrZ) Controls Twitching Motility and Biogenesis of Type IV Pili

et al. 2006

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“…That is, the deformations of helical structure occur in the context of the water molecules, proteins, and other species in direct contact with the double helix. Prior to our work, analyses of such interactions were literal and statistical in the sense of counting the number of different contacts in known structures 13,14 , or protein-centric in the sense of cataloging the various amino acids and folding motifs in close contact with nucleic acid [15][16][17][18] . Many of the tools developed to visualize protein-DNA complexes, e.g., NUCPLOT 19 , similarly focus on the identities of amino acids or secondary structural elements with respect to DNA primary structure.…”

Section: Introductionmentioning

confidence: 99%

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

2008

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We present a set of protocols showing how to use the 3DNA suite of programs to analyze, rebuild, and visualize three-dimensional nucleic-acid structures. The software determines a wide range of conformational parameters, including the identities and rigid-body parameters of interacting bases and base-pair steps, the nucleotides comprising helical fragments, the area of overlap of stacked bases, etc. The reconstruction of three-dimensional structure takes advantage of rigorously defined rigid-body parameters, producing rectangular block representations of the nucleic-acid bases and base pairs and all-atom models with approximate sugar-phosphate backbones. The visualization components create vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The utility programs use geometric variables to control the view and scale of an object, for comparison of related structures. The commands run in seconds even for large structures. The software and related information are available at http://3dna.rutgers.edu/.

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“…Positions 3, 5, and 7, shown in bold, are proposed to contact bases in the major groove of the DNA site. The model is reasonably consistent with general observations and models regarding ␤-sheet DNA-binding proteins (76,79). C. Repressors.…”

Section: Resultsmentioning

confidence: 99%

Percolation of the Phd Repressor-Operator Interface

Zhao

Magnuson

2005

J Bacteriol

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Transcription of the P1 plasmid addiction operon, a prototypical toxin-antitoxin system, is negatively autoregulated by the products of the operon. The Phd repressor-antitoxin protein binds to 8-bp palindromic Phd-binding sites in the promoter region and thereby represses transcription. The toxin, Doc, mediates cooperative interactions between adjacent Phd-binding sites and thereby enhances repression. Here, we describe a homologous operon from Salmonella enterica serovar Typhimurium which has the same pattern of regulation but an altered repressor-operator specificity. This difference in specificity maps to the seventh amino acid of the repressor and to the symmetric first and eighth positions of the corresponding palindromic repressor-binding sites. Thus, the repressor-operator interface has coevolved so as to retain the interaction while altering the specificity. Within an alignment of homologous repressors, the seventh amino acid of the repressor is highly variable, indicating that evolutionary changes in repressor specificity may be common in this protein family. We suggest that the robust properties of the negative feedback loop, the fuzzy recognition in the operator-repressor interface, and the duplication and divergence of the repressor-binding sites have facilitated the speciation of this repressor-operator interface. These three features may allow the repressoroperator system to percolate within a nearly neutral network of single-step mutations without the necessity of invoking simultaneous mutations, low-fitness intermediates, or other improbable or rate-limiting mechanisms.Bacteriophage P1 can be transmitted horizontally, as a viral particle, or vertically, as the P1 plasmid prophage (36). The low-copy-number P1 plasmid (61) is remarkably stable (67) due to faithful replication (6), partition (5), resolution (7), and addiction (43) functions. Replication and resolution system functions act to maintain a copy number of approximately one to two separate plasmid molecules per chromosome, while the partition function ensures that each daughter cell gets at least one plasmid copy. Should these systems fail, the P1 plasmid addiction operon, a classic toxin-antitoxin system, acts to arrest the plasmid-free cell. Elimination or arrest of plasmid-free cells may leave more resources for plasmid containing cells (17,74).The P1 plasmid addiction operon encodes a 73-amino-acid repressor-antitoxin, Phd, which prevents host death, and a 126-amino-acid toxin, Doc, which is responsible for death on curing (plasmid loss) (43). The Phd antitoxin is both synthesized (43) and degraded at a higher rate than the toxin, Doc. Degradation of Phd is dependent upon the host-encoded, ATP-dependent ClpXP protease (44). While the plasmid is maintained, there is enough antitoxin present to neutralize the toxin. When the plasmid is lost or if expression is halted due to some other cause, the continuing degradation of the antitoxin, in the absence of new synthesis, unveils the toxin and thus arrests the cell.Transcription of the P1 p...

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DNA recognition by β‐sheets

Cited by 11 publications

References 0 publications

The Pseudomonas aeruginosa Ribbon-Helix-Helix DNA-Binding Protein AlgZ (AmrZ) Controls Twitching Motility and Biogenesis of Type IV Pili

The Pseudomonas aeruginosa Ribbon-Helix-Helix DNA-Binding Protein AlgZ (AmrZ) Controls Twitching Motility and Biogenesis of Type IV Pili

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

Percolation of the Phd Repressor-Operator Interface

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