explanation of different binding motiffs and their structures

1. DNA BINDING MOTIFFS
D.INDRAJA

2. DNA binding motifs
• These are the DNA binding proteins can make specific contacts to dsDNA molecule without breaking the
hydrogen bonds
• DNA-binding proteins such as transcription factors recognize and bind a short nucleotide sequence
usually as a result of extensive complementarity between the surface of the protein and surface features of
the double helix in the region of binding
• Contacts occur between the DNA binding proteins and the edges of the base pairs that are exposed in the
grooves of the DNA especially the major groove
• Several conserved structural motifs have been identified which are common to many different DNA
binding proteins with quiet different specificities ,some of them are

4. • First DNA-binding protein motif identified
• It comprises about 20 amino acids in two short α helices, each 7-9 amino acids residues long, separated
by β-turn and is found in many proteins that regulate gene expression.
• First identified in 3 prokaryotic proteins: two repressor proteins (Cro and cI) and the E. coli catabolite
activator protein (CAP).
• This structure generally is not stable by itself, it is simply the reactive portion of somewhat larger DNA-
binding domain. One of the 2 helices is recognition helix because it usually contains many of the amino
acids that interact with the DNA in a sequence specific way. When bound to DNA, the recognition helix
is positioned in or nearly in the major groove. The lambda repressor and Cro proteins control
bacteriophage lambda gene expression, and the tryptophan repressor and the catabolite activator protein
(CAP) control the expression of sets of E. coli genes.

6. • About 30 amino acids residues form an elongated loop held together at the base by a single Zn2+ ion,
coordinated to four of the 2 residues (four Cys, or two Cys and two His).
• Zinc does not itself interact with DNA.
• The coordination of Zinc with the amino acid residues stabilizes this small structural motif.
• The interaction of a single Zinc finger with DNA is typically weak.
• DNA-binding proteins like Zif268 have multiple Zinc fingers that enhance binding by interacting
simultaneously with DNA.
1.Zinc finger domain exists in two forms:
C2H2 zinc finger:
• A loop of 12 amino acids anchored by two cysteine and two histidine
residues that tetrahedrally co- ordinate a zinc ion. This motif folds
into a compact structure comprising two β-strands and one α-helix.
• The α-helix containing conserved basic amino acids binds in the
major groove of DNA.
Examples: (1) TFIIIA, the RNA Pol III transcription factor, with
C2H2 zinc finger repeated 9 times. (2) SP1, with 3 copies of C2H2
zinc finger. Usually, three or more C2H2 zinc fingers are required for
DNA binding

7. 2. C4 zinc finger:
• zinc ion is coordinated by 4 cysteine residues.
• Example: Steriod hormone receptor transcription factors consisting of homo- or hetero-dimers, in which
each monomer contains two C4 zinc finger.

9. • This motif is an amphipathic α-helix with a series of hydrophobic amino acid residues concentrated on
one side the hydrobhobic surface forming an area of contact between the two polypeptides of a dimer.
• Stricking feature : Leu residue at every seventh position form a straight chain along the hydrophobic
surface.
Regulatory proteins with leucine zippers
• DNA binding domain with a high concentration of Lsy or Arg residues
• interact with negatively charged phosphates of the DNA backbone
• Leucine zippers have been found in many eukaryotic and a few bacterial proteins