Zinc-fingers

TFIIIA has nine zinc fingers, but other proteins have anything from one to more than 60 zinc finger motifs within their sequence. 

The classic zinc fingers bind to DNA in tandem along the major groove... 

It has also been possible to determine the x-ray structures of classic zinc finger motifs from several proteins bound to specific DNA fragments. We will here describe one such structure containing three zinc fingers from a mouse protein, Zif 268, which is expressed at an early developmental stage of the mouse. Nikola Pavletich and Carl Pabo at the Johns Hopkins University School of Medicine, Baltimore, determined the x-ray structure to 2.1 A resolution of a recombinant polypeptide derived from Zif 268 bound to a 10-base... 

Figure 10.2 (a) Amino acid sequence of a fragment of the Zif 268 protein that contains three zinc fingers. Residues forming the p strands and a helices are red and green, respectively, and those involved in the turn between the last p strand and the a helix are blue, (b) The nucleotide sequence of the DNA fragment that was used in the x-ray structure determination of the Zif 268 fragment complexed with DNA. 

Figure 10.3 Schematic diagram of the stmcture of three zinc fingers of Zif 268 bound to DNA. The three zinc fingers, which bind In tandem to the major groove of DNA, are colored blue, red and green from the N-terminus. The zinc fingers have the same stmcture and bind in a similar way with the N-terminus of the a helix pointing into the major groove. (Adapted from N.P. Pavletich et al.. Science 261 1701-1707, 1993.)...

The finger region of the classic zinc finger motif interacts with DNA... 

The 12 residues between the second cysteine zinc ligand and the first histidine ligand of the classic zinc finger motif form the "finger region". Structurally, this region comprises the second p strand, the N-terminal half of the helix and the two residues that form the turn between the p strand and the helix. This is the region of the polypeptide chain that forms the main interaction area with DNA and these interactions are both sequence specific. 

Figure 10.4 Detailed view of the binding of the second zinc finger of Zif 268 to DNA. Two side chains, Arg 46 and His 49, form sequence-specific interactions with DNA. There are also three nonspecific interactions between phosphate groups of the DNA and the side chains of Arg 42, Ser 45, and His 53.

Figure 10.5 Comparison of the sequence-specific binding to DNA of six different zinc fingers. Residues in the N-terminus of the a helix in the finger regions are numbered 1 to 6. The residue immediately preceding the a helix is numbered -1. Amino acid residues and nucleotides that make sequence-specific contacts are colored. In spite of the structural similarities between the zinc fingers and their overall mode of binding, there is no simple rule that governs which bases the fingers contact.

Fairall, L., et al. The crystal structure of a two zinc finger peptide reveals an extension to the rules for zinc finger/DNA recognition. Nature 366 483-487, 1993. 

Lee, M.S., et al. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245 635-637, 1989. 

Pavletich, N.P., Pabo, C.O. Crystal structure of a five-finger GLI-DNA complex new perspectives on zinc fingers. Science 261 1701-1707, 1993. 

The ultimate goal of protein engineering is to design an amino acid sequence that will fold into a protein with a predetermined structure and function. Paradoxically, this goal may be easier to achieve than its inverse, the solution of the folding problem. It seems to be simpler to start with a three-dimensional structure and find one of the numerous amino acid sequences that will fold into that structure than to start from an amino acid sequence and predict its three-dimensional structure. We will illustrate this by the design of a stable zinc finger domain that does not require stabilization by zinc. 

The classic zinc fingers, the DNA-binding properties of which are discussed in Chapter 10, are small compact domains of about 30 residues that fold into an antiparallel p hairpin followed by an a helix. All known classic zinc fingers have a zinc atom bound to two cysteines in the hairpin and two histidines in the helix, creating a sequence motif common to all zinc finger genes. In the absence of zinc the structure is unfolded. 

Table 17.2 Amino acid sequences of the second zinc finger of Zif 268 and the designed peptide FSD-1...

The optimal sequence obtained, called FSD-1 for full sequence design, is shown in Table 17.2 and compared with the sequence of the template Zif 268. A search of the FSD-1 sequence against protein databases did not reveal a statistically significant similarity with any other protein, including zinc finger proteins. 

Figure 17.15 Schematic diagrams of the main-chain conformations of the second zinc finger domain of Zif 268 (red) and the designed peptide FSD-1 (blue). The zinc finger domain is stabilized by a zinc atom whereas FSD-1 is stabilized by hydrophobic interactions between the p strands and the a helix. (Adapted from B.I. Dahiyat and S.L. Mayo, Science 278 82-87, 1997.)...

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