Crystal Structure of
            <i>lac</i>
            Repressor Core Tetramer and Its Implications for DNA Looping

Friedman, Alan M.; Fischmann, Thierry O.; Steitz, Thomas A.

doi:10.1126/science.7792597

Cited by 298 publications

(379 citation statements)

References 63 publications

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“…3). The structure of the core tetramer does not implicate this face to be involved in tetramerization (Friedman et al 1995), and other repressors in the alignment function as dimers.…”

Section: Comparison Of Sift With Blosum62 Predictions On Laci Mutatiomentioning

confidence: 82%

Predicting Deleterious Amino Acid Substitutions

Ng¹,

Henikoff²

2001

Genome Res.

2,332

2,014

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Many missense substitutions are identified in single nucleotide polymorphism (SNP) data and large-scale random mutagenesis projects. Each amino acid substitution potentially affects protein function. We have constructed a tool that uses sequence homology to predict whether a substitution affects protein function. SIFT, which sorts intolerant from tolerant substitutions, classifies substitutions as tolerated or deleterious. A higher proportion of substitutions predicted to be deleterious by SIFT gives an affected phenotype than substitutions predicted to be deleterious by substitution scoring matrices in three test cases. Using SIFT before mutagenesis studies could reduce the number of functional assays required and yield a higher proportion of affected phenotypes. SIFT may be used to identify plausible disease candidates among the SNPs that cause missense substitutions.

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“…3). The structure of the core tetramer does not implicate this face to be involved in tetramerization (Friedman et al 1995), and other repressors in the alignment function as dimers.…”

Section: Comparison Of Sift With Blosum62 Predictions On Laci Mutatiomentioning

confidence: 82%

Predicting Deleterious Amino Acid Substitutions

Ng¹,

Henikoff²

2001

Genome Res.

2,332

2,014

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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%

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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“…This method has recently revealed 136,149 the presence of two-looped states which is consistent with the presence of multiple configurations observed using FRET, 150,151 electron microscopy studies 152 and suggested by X-ray crystallography studies. 116 All of these experiments suggest an important role for protein flexibility. A more sophisticated technique which has been successfully applied to Gal repressor is the magnetic tweezer assay.…”

mentioning

confidence: 94%

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

et al. 2006

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The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA persistence length. Similarly, eukaryotic DNA is packed in DNA-protein complexes (nucleosomes) in which DNA is tightly bent around protein spools. DNA is also tightly bent by many proteins that regulate transcription, resulting in a variation in gene expression that is amenable to quantitative analysis. In these cases, DNA loops are formed with lengths that are comparable to or smaller than the DNA persistence length. The aim of this review is to describe the physical forces associated with tightly bent DNA in all of these settings and to explore the biological consequences of such bending, as increasingly accessible by single-molecule techniques.

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Crystal Structure of lac Repressor Core Tetramer and Its Implications for DNA Looping

Cited by 298 publications

References 63 publications

Predicting Deleterious Amino Acid Substitutions

Predicting Deleterious Amino Acid Substitutions

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

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

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