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BOYLE ERICA
13/SCI03/005
BCH 415- BIO INORGANIC CHEMISTRY.
ASSIGNMENT: WRITE ON ZINC FINGERS.
The zinc finger is a common structural motif in many protein DNA binding
domains. It is found in roughly 3%(!) of all proteins and performs a diverse
range of functions not limited to enhancing or inhibiting one specific gene.
They are one of several domains that evolved to solve the problem of sequence
specific binding of nucleic acids. A zinc ion coordinates with the protein and
helps stabilize an alpha helix that can recognize DNA in a sequence specific
manner. The common thread among these domains is a requirement for a
coordinated zinc ion and a sequence specific interaction with nucleic acids like
DNA or RNA (usually), but the structure of the other domains determines how
the protein uses this interaction to perform its cellular functions.
The Structure
Zinc finger domains take advantage of the coordination of a zinc ion to cysteine
and histidine side chains (in the "classic zinc finger" but there are other
uncommon variations as well) to stabilize a short alpha helix and two beta
sheets. The alpha helix is oriented in such a way that it fits neatly into the major
groove of DNA where it orients side chains towards the unique functional
groups on the edge of DNA bases. Side chains on the zinc finger helices (the
"finger") hydrogen bond with only the correct DNA base, and thus bind to DNA
in a sequence specific manner.
The following are images of a single zinc finger protein (Zif268, pdb ID: 1ZAA
[1]) with three zinc finger domains (green) coordinated to zinc ions (gray) by
the side chains of two cysteines and two histidines (blue). Each zinc finger
domain has an alpha helix whose side chains (yellow) interact with individual
bases in the major groove of double stranded DNA (orange) through hydrogen
bonding interactions (red).
Notice the coordination chemistry of the zinc ion with the cysteines in the loop
and the histidines in the alpha helix. This coordination chemistry stabilizes the
"finger" and allows it to contact DNA. Also notice that multiple zinc finger
domains can wrap around the DNA with each contacting the major groove.
Looking down the center of DNA shows the yellow side chains of the zinc
finger protein pointing in towards the DNA along the major groove.
Zooming in on the major groove shows the sequence specific interactions
between zinc finger side chains and the major groove functional groups of the
purines in the DNA. These hydrogen bond contacts are lost if the sequence of
the DNA doesn't exactly match the side chains of the zinc finger and vice versa.
The Function
The structure of the zinc finger explains its common function in stabilizing the
recognition helix that confers sequence specific recognition of nucleic acids.
Zinc fingers are easily modified protein motifs; minor changes to the amino
acids in the helix with side chains that contact DNA can alter the sequence
specificity. Nature has found many uses for these short, highly specific, easily
modifiable and evolvable, sequence motifs when a protein needs to recognize a
specific RNA or DNA sequence to function properly. They are especially
common domains in transcription factors that must recognize specific DNA
sequences upstream of a target gene to either inhibit or enhance binding of RNA
polymerase or other transcription factors. They can either enhance or inhibit the
transcription of the gene into mRNA depending on where they bind and which
other proteins they recruit.
Other functions that proteins with zinc finger domains are used for in the cell:
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The transcription factor TFIIIA has up to 9 zinc fingers that interact with
the promoter sequence of DNA where it recruits RNA polymerase and
induces transcription of the 5S rRNA gene.
The SLUG and SNAIL zinc finger proteins bind at an E-box sequence on
DNA and repress transcription of E-cadherins by blocking the access of
other transcription factors that would otherwise promote its transcription.
The PARP protein has two zinc finger domains that bind specifically to
DNA sites with single strand breaks and a catalytic domain that repairs the
damage.
Tristetraprolin (aka ZFP36) is a translational regulator whose zinc finger
domain binds to specific sequences of AU-rich elements in the 3'
untranslated region of mRNAs and targets them for degradation.
Zinc-finger antiviral protein (ZAP) binds specific sequences of viral
mRNAs and recruits the RNA exosome to break them down before they are
translated.
The Future
Zinc finger domains are so easy to modify while retaining sequence specificity
for DNA that bioengineers have been able to design zinc fingers that bind to
most three base pair sequence with high specificity.[2] Most recent work on
zinc fingers focuses on engineering them to perform novel biological functions
to specific DNA sequences (restriction endonucleases, inhibitors to fight viral
mRNAs, and more).
References:
1. Pavletich, N. & Pabo, C. Zinc finger-DNA recognition: crystal structure
of a Zif268-DNA complex at 2.1 A. Science 252, 809-817 (1991).
2. Segal, D.J. Toward controlling gene expression at will: Selection and
design of zinc finger domains recognizing each of the 5’-GNN-3’DNA
target sequences. Proceedings of the National Academy of Science 96,
2758-2763(1999).
3. http://quora.com