Improved detection of helix-turn-helix DNA-binding motifs in protein sequences

Dodd, Ian B.; Egan, J. Barry

doi:10.1093/nar/18.17.5019

Cited by 518 publications

(363 citation statements)

References 60 publications

Supporting

Mentioning

351

Contrasting

Order By: Relevance

“…This model is consistent with the biochemical data that indicate that the DNA is wrapped around a core of protein (13,15). It has been suggested that a putative helix-turn-helix motif in the center of ParB binds the box A motif (28,29). In this case, these regions of each monomer would be directed toward box A2 and A3 (which make an inverted repeat sequence) but would be positioned on one side of the IHF bend rather than flanking it.…”

Section: Discussionsupporting

confidence: 89%

Stoichiometry of P1 Plasmid Partition Complexes

Bouet

Surtees

Funnell

2000

Journal of Biological Chemistry

View full text Add to dashboard Cite

The P1 plasmid prophage is faithfully partitioned by a high affinity nucleoprotein complex assembled at the centromere-like parS site. This partition complex is composed of P1 ParB and Escherichia coli integration host factor (IHF), bound specifically to parS. We have investigated the assembly of ParB at parS and its stoichiometry of binding. Measured by gel mobility shift assays, ParB and IHF bind tightly to parS and form a specific complex, called I ؉ B1. We observed that as ParB concentration was increased, a second, larger complex (I ؉ B2) formed, followed by the formation of larger complexes, indicating that additional ParB molecules joined the initial complex. Shift Western blotting experiments indicated that the I ؉ B2 complex contained twice as much ParB as the I ؉ B1 complex. Using mixtures of ParB and a larger polyhistidine-tagged version of ParB (His-ParB) in DNA binding assays, we determined that the initial I ؉ B1 complex contains one dimer of ParB. Therefore, one dimer of ParB binds to its recognition sequences that span an IHF-directed bend in parS. Once this complex forms, a second dimer can join the complex, but this assembly requires much higher ParB concentrations.

show abstract

Section: Discussionsupporting

confidence: 89%

Stoichiometry of P1 Plasmid Partition Complexes

Bouet

Surtees

Funnell

2000

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…In silico methods Domain predictions were made using InterProScan (Mulder et al, 2007), HTH program (Dodd and Egan, 1990) and BLASTP (Altschul et al, 1990). Precise length of the domains was determined using CDD (Marchler-Bauer et al, 2007).…”

Section: Integrating Promoter Fusions On the M Acetivorans Chromosomementioning

confidence: 99%

Regulation of putative methyl‐sulphide methyltransferases in Methanosarcina acetivorans C2A

Bose

Kulkarni

Metcalf

2009

Molecular Microbiology

View full text Add to dashboard Cite

SummaryThe regulation of the Methanosarcina acetivorans mtsD, mtsF and mtsH genes, which encode putative corrinoid/methyltransferase isozymes involved in methylsulphide metabolism, was examined by a variety of methods, suggesting that their expression is regulated at both the transcriptional and posttranscriptional levels. Transcripts of all three genes, measured by quantitative reverse transcription PCR, were shown to be most abundant during growth on methanol with dimethylsulphide (DMS). Transcript levels were also high in media with CO or methylamines, but much lower with methanol. In contrast, translational fusions to mtsD showed high expression levels on CO or methanol with DMS, while the mtsF translational fusion showed highest reporter gene activity on methylamines with much lower expression on CO or methanol with DMS. The activity of mtsD and mtsF fusions was very low when the strains were grown in methanol or acetate. Expression of the mtsH fusion was not detected on any substrate, despite the presence of an mRNA transcript. The transcription start sites of all three genes were determined by 5Ј-RACE revealing large leader sequences for each transcript. Characterization of deletion mutants lacking putative regulatory genes suggests that MA0862 (msrF), MA4383 (msrC) and MA4560 (msrG) act as transcriptional activators of mtsD, mtsF and mtsH respectively.

show abstract

“…This structure of two helices ( Fig. 1), now termed the helix-turn-helix DNA-binding motif, contains a tight f-turn resulting in an interhelical angle of nearly 900 and an amino acid sequence preference which has been extended to other DNAbinding proteins White, 1987;Brennan & Matthews, 1989b;Dodd & Egan, 1990). One of the helices ( Fig.…”

Section: Helix-turn-helix Proteinsmentioning

confidence: 99%