BIOINORGANIC CHEMISTRY A Short Course Second Edition

70 BIOCHEMISTRY FUNDAMENTALS

Figure 2.23 (A) Amino acid sequence and secondary structure of Zif1, Zif2, and Zif3
zinc fi ngers of Zif268. (B) Base contacts of the − 1, 1, 2, 3, 5, 6 α - helical amino acid resi-
dues of Zif1, Zif2, and Zif3. (C) DNA sequence of the TATA box strand for which zinc
fi ngers were designed. (Figures adapted with permission from Figure 1 of reference 37.
Copyright 1997, American Association for the Advancement of Science.)

Finger 1 MERPYACPVESCDRRFS E L HIRIHTGQK

Finger 2 L HIRTHTGEK

Finger 3 PFACDI-----CGRKFA E HTKIHLRQKD

antiparallelβ sheet region

α helical region

randomized positions

bold letters zinc ion ligands

bold numbers α helix residues interacting with

bases on DNA strands

Finger 1 Finger 2 Finger 3

3'T G C G G G T G C G 5'

5'A C G C C C A C G C 3'

-1 1 2 3 5 6 -1 1 2 3 5 6

R S D E T R

-1 1 2 3 5 6

R S D E K R

TATA 3' G A A A A T A T C G G5'

finger amino acid contacts within the

DNA subsite (note finger 2 D to C

contact outside subsite)

less favorable contacts from position 2

(also outside the finger's DNA subsite)

randomized fingers were selected to bind

at boxed subsites

T T T T A T A G C

-1 1 2 3 5 6

RDSTR

RDSHTT

RDSRRK

A

B C

PFQCRI-----CMRNFS

R S D H T T

a recognition code for zinc - fi nger binding to DNA. One example of such a
system — in this case the so - called Tramtrack (TTK) transcriptional regulator
from theDrosophilia development gene fushi - tarazu — is shown in Figure
2.24.^38 The TTK structural data are deposited as 2DRP in the protein data
bank (PDB).
Two identical zinc - fi nger – protein – DNA double strand interactions are
found in the 2DRP crystal ’ s unit cell. A close - up view of one of these protein –
DNA interactions is visualized in Figure 2.24. A description of the protein –