Zinc Finger Binding Protein

2007-09-20T02:49:00.001-07:00

What is a zinc finger

Protein(s) which contains at least one zinc-finger.

A small, functional, independently folded domain that requires coordination of one or more zinc ions to stabilize its structure. These proteins use Zinc ions to fold properly into "Zn Fingers". Using a series of these Fingers, the transcription factor can recoginize a specific DNA sequence. So, folding of these zinc fingers is important

In eukaryotes, often complex sets of regulatory elements control the initiation of transcription of structure genes. Upstream of the RNA polymerase II initiation site there are different combinations of specific DNA sequences, each of which is recognized by a corresponding site-specific DNA-binding protein. These protein are called transcription factor.

Transcription factors have two functionally different domains, one that binds to specific DNA sequences and another that activates transcription. And now NMR methods recently have been used to determine the 3D structure of these motifs: zinc fingers, leucine zippers, and helix-turn-helix motifs.

Structure:

One of the most abundant DNA-binding motifs. Proteins may contain more than one finger in a single chain; each motif consists of 2 anti-parallel beta-strands followed by an alpha-helix. A single zinc ion is tetrahedrally coordinated by conserved histidine and cysteine residues, stabilising the motif.

Zinc-finger-containing proteins constitute the most abundant protein super family in the mammalian genome, and are best known as transcriptional regulators. They are involved in a variety of cellular activities such as development, differentiation, and tumor suppression. The first zinc finger domain to be identified in Xenopus laevis, basal transcription factor TFIIIA (Miller et al. 1985), is the archetype for the most common form of zinc finger domain, the C2H2 domain. The three-dimensional structure of the basic C2H2 zinc finger is a small domain composed of a -hairpin followed by an -helix held in place by a zinc ion. Zinc fingers generally occur as tandem arrays, and in DNA-binding modules the number of sequential fingers determines specific binding to different DNA regions. One zinc finger binds the major groove of the double helix and interacts with 3 bp, and the minimal number of fingers required for specific DNA binding is two . One of the best characterized families of DNA-binding zinc fingers is the Sp/Krüppel-like factor. Members of this family share in common three highly conserved C2H2-type fingers in their C-terminal ends combined with transcriptional activator or repressor domains in the N terminus. Other families of DNA-binding zinc fingers differ from the C2H2-type basic module in the spacing and nature of their zinc-chelating residues (cysteine–histidine or cysteine–cysteine;. Additional families of zinc finger domains have been implicated in protein–protein interactions and lipid binding .

Zinc fingers are among the most common structural motifs in the proteome predicted from the genome sequences of Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans (Rubin et al. 2000) as well as the draft human genomic sequences.

The zinc finger domains are not only one of the most abundant domains in the eukaryotic genomes but are also one of the best examples of protein structure modularity. The abundance of zinc finger proteins in eukaryotic transcriptomes is believed to be a consequence of the high structural stability of the zinc-binding domains, the redox stability of the zinc ion to the ambient reducing conditions in a cell. These features make this domain a perfect structure for the formation of protein–protein and protein–nucleic acid complexes.

Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

● The Cys2His2 zinc finger is one of the most common DNA-binding motifs in Eukaryota. A simple mode of DNA recognition by the Cys2His2 zinc finger domain provides an ideal scaffold for designing proteins with novel sequence specificities.

● Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by cysteines and histidines.

● The zinc finger domain defines one of the largest protein superfamilies in mammalian genomes;46 different conserved zinc finger domains are listed in InterPro (http://www.ebi.ac.uk/InterPro). Zinc finger proteins can bind to DNA, RNA, other proteins, or lipids as a modular domain in combination with other conserved structures.

The zinc finger is a sequence motif involved in binding of DNA:

The C₂H₂ class

        Cys-(Xaa)₂-Cys-(Xaa)₁₂-His-(Xaa)₃-His.

Xaa - nonspecific amino acid.

This motif was first discoved in TFIIIA ( an RNA polymerase III associated transcription factor) isolated from Xenopus laevis (African clawed toad). In TFIIIA, this sequence is repeated nine times in the protein. Each repeat can coordinate a zinc ion with the two cysteines and two histidines:

        ======

       =      =

      =        =

       =      =

      CYS    HIS

       = \  / =

       =  Zn   =

      CYS/  \ =

       =     HIS

       =      =

The twelve residues between the cysteine and histidine loop out to form a DNA binding interface.

The C_x class

The C_x class of zinc fingers have a variable number of cysteines that can chelate a Zn ion. These are also involved in DNA binding such as the GAL4 protein (yeast transcripiton factor involved in galactose metabolism.) The cysteines are closely spaced and can vary from 4 to 6 in number.

        ======

       =      =

      =        =

       =      =

      CYS    CYS

       = \  / =

       =  Zn   =

      CYS/  \ =

       =     CYS

       =      =

Several different ZnF motifs have been characterised, and vary with regard to structure, as well as binding modes and affinities. ZnF motifs can coordinate one or more zinc atoms. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that ZnF motifs are stable scaffolds that have evolved specialised functions. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Most ZnF proteins contain multiple finger-like protrusions that make tandem contacts with their target molecule, often recognising extended substrates. A few of the most common structurally defined ZnF motifs are described below.

Classical (C2H2) ZnF motifs

These motifs contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2), Cys(2)HisCys (C2HC), or Cys(3)His (CCCH) residues. These are the most common DNA-binding motifs found in eukaryotic transcription factors. Transcription factors usually contain several zinc fingers (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA.

GATA-type ZnF motifs

These motifs constitute type IV ZnFs with the general sequence C-X(2)-C-X(17-20)-C-X(2)-C, followed by a highly basic region. They can be subdivided into subgroups depending upon the length of the internal loop: type IVa have a 17-residue loop (CX2CX17CX2C), while type IVb have a 18-residue loop (CX2CX18CX2C). ZnF motifs with 19 or 20-residue loops are rare and found mainly in fungi. GATA factors play essential roles in development, differentiation and control of cell growth in eukaryotes. GATA proteins often contain more than one ZnF domain, where one domain binds DNA and the other modulates DNA binding, often by binding other factors.

RanBP-type ZnF motifs

These motifs consist of two short beta hairpins that sandwich a single zinc atom, and are similar in structure to the zinc-ribbon fold. These domains were first identified in the nuclear export protein RanBP2. RanBP ZnF domains are known to interact with ubiquitin.

A20-type ZnF motifs

These motifs bind a single zinc atom and were first identified in protein A20. These motifs are known to bind to ubiquitin, but contact a different region of ubiquitin from RanBP ZnF motifs.

LIM-type ZnF motifs

LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like ZnFs, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development. Protein containing LIM ZnF domains include the adaptor protein PINCH.

MYND-type ZnF motifs

MYND domains coordinate two zinc atoms, and are named after the three proteins (Myeloid translocation protein 8, Nervy, and DEAF-1) in which they were first found. They consist of two zinc-binding motifs, the first containing a short beta-hairpin, while the second consists of two short alpha-helices. Proteins containing MYND ZnF domains include the transcriptional co-repressor protein BS69.

RING-type ZnF motifs

RING (really interesting new gene) domains coordinate two zinc atoms. Protein containing RING ZnF domains include KAP-1, PML, and several E3 ubiquitin ligases (catalyse final step of protein ubiquitination pathway).

PHD-type ZnF motifs

PHD domains coordinate two zinc atoms, and are named after the class of proteins (plant homeodomain) in which they were first found. PHD ZnF domains differ from RING-type domains in containing a highly conserved Trp residue involved in the hydrophobic core; this residue is exposed to solvent in RING-type ZnF domains. Protein containing PHD ZnF domains include Ing2 (inhibitor of growth protein 2), BPTF, Pygopus (Wnt signalling pathway), WSTF transcription factor, and Datf1 (Death-associated transcription factor 1).

TAZ-type ZnF motifs

TAZ (transcriptional adaptor zinc-binding) domains consist of two ZnF motifs form a distinct fold unrelated to other ZnFs. Protein containing TAZ ZnF domains include CBP acetyltranscferase.

Protein which contains at least one zinc finger. A small, functional, independently folded domain that requires coordination of one or more zinc ions to stabilize its structure. Zinc fingers vary widely in structure, as well as in function, which ranges from DNA or RNA binding to protein-protein interactions and membrane association.

References

Miller, J., McLachlan, A.D., and Klug, A. 1985. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4:1609 -1614.[Medline]

Rubin, G.M., Yandell, M.D., Wortman, J.R., Gabor Miklos, G.L., Nelson, C.R., Hariharan, I.K., Fortini, M.E., Li, P.W., Apweiler, R., Fleischmann, W., et al. 2000. Comparative genomics of the eukaryotes. Science 287:2204 -2215.[Abstract/Free Full Text]

EST Analysis for SSR detection

Zinc Finger Binding Protein

The C2H2 class

The Cx class

The C₂H₂ class

The C_x class