Lesk: Introduction to Genomics 
Answers to end-of-chapter exercises
Figures from the bookLesk: Introduction to Genomics
Chapter 07
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Page 386, Fig 7.7
Mouse SH3 domain c-Crk (green) complexed with peptide (pink) [1CKA].
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Page 386, Fig 7.8
Complex between human growth hormone (green) and two molecules of its receptor (red and purple). Interaction
with the hormone promotes the interaction between the two receptor molecules [3HHR].
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Page 391, Fig 7.10
Bacteriophage λ Cro is an example of the ‘helix-turn-helix’ structural motif.
Following along the chain, the first secondary structure is a helix, followed by two more helices
that frame the motif. The second of these two helices (the third helix in the molecule) – called
the recognition helix – lies in the major groove and makes extensive contacts with the DNA.
A long C-terminal tail wraps around the DNA, following the minor groove [1CRO].
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Page 392, Fig 7.11
The homeodomain antennapedia–DNA complex [9ANT]. As with many DNA-binding
proteins, an α-helix binds in the major groove of DNA. The structure of the antennapedia–DNA
complex resembles, in some respects, prokaryotic helix-turn-helix proteins such as λ Cro.
However, the tail that wraps around into the minor groove is N terminal to the helix-turn-helix
motif in antennapedia, instead of C terminal as in λ Cro.
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Page 392, Fig 7.12
Jun dimer binding to DNA [1JNM]. The proteins grip the DNA as if they were picking
it up with chopsticks. The α-helices bind in major grooves on opposite sides of the double helix.
This structure shares with λ Cro, and many other DNA-binding proteins, the symmetry of the
complex, which mimics the dyad symmetry of the DNA double helix. This requires, on the part
of the protein, formation of symmetrical dimers, and on the part of the DNA, an approximately
palindromic target sequence. For Jun dimers, the target sequence is ATGACGTCAT.
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Page 393, Fig 7.13
Zif268, a tandem three-finger structure binding the sequence GCGTGGGCG [1AAY].
Each finger interacts with three consecutive bases. In each finger, three positions along the
α-helix, non-consecutive in the amino acid sequence, contain primary determinants of the
DNA-sequence specificity.
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Page 393, Fig 7.14
Like many other DNA-binding proteins, the Met repressor binds DNA as a symmetrical dimer [1CMA]. In the complex, each monomer contributes one strand of twostranded β-sheet, which sits in the major groove, with sidechains making hydrogen bonds
to bases. The co-repressor, S-adenosyl-methionine, is required for high-affinity binding.
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Page 394, Fig 7.15
The TATA boxbinding protein [1YTB]. The obvious feature of this complex is the very strong bending and unwinding induced in the DNA. A long curved β-sheet sits against an unusually flat surface on the DNA, the result of prying open of the minor groove. Phe sidechains intercalate between the bases.
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Page 394, Fig 7.16
The structure of the DNA-binding subunit of p53 shows a double-β-sheet fold
[1TSR]. A helix sits in the major
groove and sidechains from loops
connecting strands of the β-sheet
insert into the minor groove.
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