DNA BINDING PROTEINS

Reference : BRANDEN & TOOZE

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12 Å5 Å

Proteins that bind DNA and are involved in replication or transcription and do so in a sequence specific way.

Transcription factors are dimers when active, i.e., they bind to DNA upon dimerization and are inactive in the monomeric form.

Dimerization is a regulatory mechanism of controlling transcription factor activity. 

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PROKARYOTIC DNA BINDING PROTEINS

The helix-turn-helix motif is the common DNA recognition motif in prokaryotes

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(An overview of the structures of protein-DNA complexesNicholas S Luscombe et al.,)

HTH proteins: the Cro and Repressor familyThe DNA-binding motif The protein binds as a dimerone monomer is coloured blue and the other yellow.The DNA is shown as a space-filling model.

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Lambda Cro

The monomer of Cro from bacteriophage Lambda consists of 66 amino acidsContains three alpha helices and three beta strands. In the dimer there is an antiparallel alignment of the C-terminal strand of each subunit, giving a six-stranded antiparallel sheet.

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April 9, 2023 8Branden & Tooze - Pg 130

Alpha helices 2 and 3 that form the helix-turn-helix motif are coloured blue and red, respectively.

(D. Ohlendorf at al., J. Mol. Biol. 169: 757-769, 1983.)

Cro Monomer

Branden & Tooze - Pg 132

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Cro DimerThe main dimer interactions are between between strands 3 from each subunit.

One subunit is green and the other is brown.

Alpha helices 2 and 3, the helix-turn-helix motifs, are coloured blue and red, respectively, in both subunits.

(D. Ohlendorf et al., J. Mol. Biol. 169: 757-769, 1983.)

Branden & Tooze - Pg 132

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Protein Motifs: the Helix‐Turn‐Helix MotifBrian W Matthews, Howard Hughes Medical Institute and University of Oregon, Oregon, USA

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Lambda Repressor The repressor is a dimer of a 236

amino acid subunit. Each subunit consists of two domains,

one of which (the N-terminal) includes the helix-turn-helix motif and binds DNA, while the other is responsible for the formation of dimers.

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Repressor Monomer

The N-terminal domain of lambda repressor, which binds DNA, contains 92 aa residues folded in to 5 alpha helices

Two of these, alpha 2 & 3 (blue and red) form a HTH motif similar to Cro

(C. Pabo and M. Lewis, Nature 298: 443-447, 1982.)

Branden & Tooze - Pg 133April 9, 2023 13

Repressor dimer

One subunit is green and the other is brown.

Alpha helices 2 and 3, the helix-turn-helix motifs, are colored blue and red, respectively, in both subunits.

(C. Pabo and M. Lewis, Nature 298: 443-447, 1982.)Branden & Tooze - Pg 133

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Protein Motifs: the Helix‐Turn‐Helix MotifBrian W Matthews, Howard Hughes Medical Institute and University of Oregon, Oregon, USA

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trp Repressor

The trp repressor is a DNA-binding protein which regulates tryptophan synthesis in E. coli .It is dimeric but unlike the dimers described so far, the conformation of the individual subunits is not compact, and does not occur in isolation. The chain consists of six alpha helices, including the DNA-binding helix-turn-helix motif.

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107 aa residues that are folded into 6 alpha helices.

Alpha helices 4 and 5, the helix-turn-helix motifs, are coloured blue and red

trp Repressor

Branden & Tooze - Pg 142April 9, 2023 17

A conformational change operates a functional switch

Branden & Tooze - Pg 143April 9, 2023 18

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The regulation of this gene involves negative feedback: trp repressor only binds to DNA when a L-tryptophan molecule is bound to each subunit. Each tryptophan binds between helices 3 and 5 and causes an allosteric change in the protein conformation so that its helices are in the correct orientation, 34Å apart, for interaction with the major groove. In the absence of tryptophan, the recognition helices are folded inwards towards the central core of the protein and they no longer can simultaneously fit into the groove. Therefore the repressor cannot bind, and L-tryptophan synthesis proceeds.

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