Ferguson ZNF Sandbox

spinqualitylabelsall models PDB ID 1znf Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
1znf, 37 NMR models ()
Ligands:
Non-Standard Residues:	,
Structural annotation: Resources: UniProt : P08045
Resources:	FirstGlance, OCA, RCSB, PDBsum
Coordinates:	save as pdb, mmCIF, xml

The Zinc FingerThe Zinc Finger

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in Xenopus laevis, the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain and . These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

Zinc Finger StructureZinc Finger Structure

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure . Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. .

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores.

spinqualitylabelsall models PDB ID 1tf6 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
1tf6, resolution 3.10Å ()
Ligands:
Structural annotation: Resources: InterPro : Ipr013087, Ipr015880, Ipr007087 Pfam : PF00096 SCOP : d1tf6a5, d1tf6a2, d1tf6a6, d1tf6a3, d1tf6a4, d1tf6a1, d1tf6d5, d1tf6d6, d1tf6d3, d1tf6d4, d1tf6d1, d1tf6d2 UniProt : P03001
Functional annotation: Cellular component: intracellular nucleus Biological process: transcription regulation of transcription, DNA-dependent Molecular function: DNA binding nucleic acid binding metal ion binding RNA binding zinc ion binding
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, RCSB, PDBsum
Coordinates:	save as pdb, mmCIF, xml

DNA BindingDNA Binding

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities.

SpecificitySpecificity

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix . Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

DNA Binding in mutant zinc finger domainsDNA Binding in mutant zinc finger domains

Two mutants in the N-terminal domain of ADR1, a yeast transcription factor that contains two Cys2-His2 zinc finger sequences spanning residues 102-159 were studied at the Department of Biochemistry at the University of Washington. The structure to the left shows the region responsible for DNA binding and contains two zinc fingers. Within this region, there are two point mutants at position 118 in the N-terminal zinc finger (ADR1b: 102-130) that adversely affect the DNA-binding activity of ADR1 that been identified: H118A and H118Y. Comparisons of wild-type ADR1b and the two mutants revealed that neither mutation causes a significant structural perturbation. The structures indicate that the DNA binding properties of the His 118 mutants are dependent on the identity of the side chain at position 118, which makes a direct DNA contact in the wild-type ADR1 protein. The results suggest that the identity of the side chain at the middle DNA contact position in Cys2-His2 zinc fingers may be changed regarding the domain structure and this change can and will affect the affinity of the protein-DNA interaction.

Other Folds in Zinc FingersOther Folds in Zinc Fingers

There is a large variety of folding patterns of the zinc finger protein. These patterns have been classified into eight different folding groups based on chain conformation and secondary structure. Several of these fold groups are presented below

Gag KnuckleGag Knuckle

is classified by two beta strands connected by a turn, known as the zinc knuckle, with a loop. Gag knuckles are shorter than the classical domains, with only about 20 residues instead of the usual 30 residues.

Treble Clef FingerTreble Clef Finger

The consists of a beta hairpin at the N terminus as well as an alpha helix at the C terminus. Treble clef fingers, which are found to be incorporated in multi-domain proteins, are present in a diverse group of proteins that frequently do not share sequence and functional similarity with each other.

Zinc RibbonZinc Ribbon

In the , the ligands for binding are contributed by two zinc knuckles. The structure contains two beta hairpins, forming two similar sites. One of these hairpins is called the primary beta hairpin and contains the N-terminal zinc sub-site, such as the transcription factor TFIIB and transcriptional elongation factor SII.

Designer Zinc Fingers to Create DNA ScissorsDesigner Zinc Fingers to Create DNA Scissors

A breakthrough in the studies of zinc finger proteins has been the ability to cleave sites in a large genome through endonuclease activities. FokI endonuclease has two domans; one that binds to DNA and another that cleaves the DNA. By fusing a FokI mononmer with two zinc finger proteins, which bind adjacent sequences, the complex will generate at least an 18 base pair sequence specific DNA nuclease that allows for selective targeting in mammalian genomes

This figure is from Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted.