Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

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β SHEET DNA RECOGNITION PROTEINS
In the other DNA-binding motifs displayed in this panel, α helices are the primary mechanism used to recognize specific DNA
sequences. In one large group of transcription regulators, however, a two-stranded β sheet, with amino acid side chains
extending from the sheet toward the DNA, reads the information on the surface of the major groove. As in the case of a
recognition α helix, this β-sheet motif can be used to recognize many different DNA sequences; the exact DNA sequence
recognized depends on the sequence of amino acids that make up the β sheet. Shown is a transcription regulator that binds
two molecules of S-adenosyl methionine (red). On the left is a dimer of the protein; on the right is a simplified diagram
showing just the two-stranded β sheet bound to the major groove of DNA.
C
DNA
ZINC FINGER PROTEINS
N N
This group of DNA-binding motifs includes one
or more zinc atoms as structural components.
All such zinc-coordinated DNA-binding motifs
are called zinc fingers, referring to their
appearance in early schematic drawings (left).
They fall into several distinct structural groups,
C
only one of which we consider here. It has a
simple structure, in which the zinc atom holds
an α helix and a β sheet together (middle). This
type of zinc finger is often found in clusters
with the α helix of each finger contacting the
major groove of the DNA, forming a nearly
continuous stretch of α helices along that
groove. In this way, a strong and specific
DNA–protein interaction is built up through a
COOH NH 2 repeating basic structural unit. Three such
C
fingers are shown on the right.
N
Y
K
His
K
Cys
H
C
COOH
R
V
G
Zn
Zn
Q
L
Zn
H
C
R
E
His
Cys
Zn
S
Zn
R
L
DNA
A
S
S
F
N
K
E
V
NH 2
HELIX–LOOP–HELIX PROTEINS
C
C
Related to the leucine zipper, the helix–loop–helix
motif consists of a short α helix connected by a loop
(red) to a second, longer α helix. The flexibility of the
loop allows one helix to fold back and park against
the other thereby forming the dimerization surface.
As shown, this two-helix structure binds both to DNA
and to the two-helix structure of a second protein to
create either a homodimer or a heterodimer. Two α
helices that extend from the dimerization interface
make specific contacts with the major groove of DNA.
DNA
loop
N
N