Zinc finger protein

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Lecture No. 12
Zinc protein motifs
Course Leaders: Dr. Judy Jays

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Lecture No. 12
• At the end of this lecture, student will be able to
• Describe the Zinc protein motifs

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Zinc finger
• A Zinc finger is a small protein structural motif that is characterized
by the coordination of one or more zinc ions (Zn2+) in order to
stabilize the fold
• It was originally coined to describe the finger-like appearance of a
hypothesized structure from the African clawed frog (Xenopus laevis)
transcription factor IIIA.
• However, it has been found to encompass a wide variety of differing
protein structures in eukaryotic cells.
• Xenopus laevis TFIIIA was originally demonstrated to contain zinc
and require the metal for function in 1983, the first such reported
zinc requirement for a gene regulatory protein followed soon
thereafter by the Krüppel factor in Drosophila. It often appears as a
metal-binding domain in multi-domain proteins.

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Zinc finger
• Cartoon representation of the Cys2His2 zinc finger motif, consisting
of an α helix and an antiparallel β sheet. The zinc ion (green) is
coordinated by two histidine residues and two cysteine residues.

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Types
• Proteins that contain zinc fingers (zinc finger proteins) are classified
into several different structural families
• There are a number of types of zinc fingers, each with a unique
three-dimensional architecture
• A particular zinc finger protein's class is determined by this three-
dimensional structure, but it can also be recognized based on the
primary structure of the protein or the identity of the ligands
coordinating the zinc ion
• In spite of the large variety of these proteins, however, the vast
majority typically function as interaction modules that bind DNA,
RNA, proteins, or other small, useful molecules, and variations in
structure serve primarily to alter the binding specificity of a particular
protein

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Classes
• Initially, the term zinc finger was used solely to describe DNA-binding
motif found in Xenopus laevis; however, it is now used to refer to any
number of structures related by their coordination of a zinc ion. In
general, zinc fingers coordinate zinc ions with a combination of
cysteine and histidine residues
Cys2His2
Two ligands from a
knuckle and two
more from the c
terminus of a helix
Gag knuckle
Two ligands from
a knuckle and
two more from a
short helix or
loop
Zinc ribbon
Two ligands
each from two
knuckles
Zn2/Cys6
Two ligands from the
N terminus of a helix
and two more from a
loop

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Functions
Diverse functions
• DNA recognition
• RNA packaging
• Transcriptional activation
• Regulation of apoptosis
• Protein folding and assembly
• Lipid binding

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Applications
• Zinc-finger proteins that recognize novel DNA sequences are the
basis of a powerful technology platform with many uses in drug
discovery and therapeutics
• Zep, a novel 49 kDa zinc finger protein, was found in the brain of day-
13 mouse embryos and cloned. Zep contains two C2H2-type zinc
finger motifs close to the N-terminal region
• ZEP-mediated regulation of endogenous genes could make it possible to use
genes in a drug discovery application that would otherwise require securing
IPR for a corresponding complementary DNA sequence
• ZEP transcription factors are made by combining the ZEPs with domains that
either activate or repress genes. ZPF TFs are used in drug discovery to
regulate genes for target validation, HTS and therapeutics
• The most common applications for engineered zinc finger arrays
include zinc finger transcription factors and zinc finger nucleases

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Zinc-finger TFs
• Zinc finger transcription factors are sequence-
specific DNA binding proteins that regulate
transcription. They possess DNA-binding domains
that are formed from repeated Cys2His2 zinc
finger motifs
• The most common DNA-binding motif in human
and multicellular animal TFs is the zinc finger
• Two types of zinc finger TFs are discussed here--
C2H2 zinc finger TFs and C4 zinc finger TFs Most
TFs that contain C2H2 zinc fingers are monomeric
• Its 2 cysteine and 2 histidine residues bind to zinc
ions (Zn2), and the a-helix containing the 2
histidines binds to bases in the major groove.
• Much less common are TFs containing C4 zinc
fingers. Most TFs containing this motif are
dimeric. Nuclear receptors, which bind steroid
hormones and other compounds, contain this
motif. The glucocorticoid receptor is shown in Fig.
b. Zinc ions are bound to the DNA recognition
helix of this motif, which contacts bases in the
major groove.

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DNA-Protein Interaction
1.Different protein motifs binding to DNA: Helix-turn-Helix motif;
the homeodomain; leucine zipper; helix-loop-helix; zinc finger
2.Dimerization approach
3.Biotechnology to identify protein and DNA sequence interacting
each other.

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Helix-turn-Helix
C-terminal binds to major groove, N-terminal helps
to position the complex, discovered in Bacteria

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Zinc Finger Motifs
Utilizing a zinc in the center
An alpha helix and two beta sheet

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Three Zinc Finger Motifs forming the
recognition site

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A dimer of the zinc finger domain of the glucocorticoid receptor (belonging to
intracellular receptor family) bound to its specific DNA sequence
Zinc atoms stabilizing DNA-binding Helix and dimerization interface

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Beta sheets can also recognize DNA sequence
(bacterial met repressor binding to s-adenosyl methionine)

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Leucine Zipper Dimer
Same motif mediating both DNA
binding and Protein dimerization
(yeast Gcn4 protein)

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Homodimers and heterodimers can
recognize different patterns
Helix-loop-Helix (HLH) Motif and its dimer

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Truncation of HLH tail (DNA binding domain) inhibits binding

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Six Zinc Finger motifs and their interaction with DNA

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Summary
• Helix-turn-Helix, homeodomain, leucine zipper, helix-loop-helix, zinc-
finger motif
• Homodimer and heterodimer
• Techniques to identify gene sequences bound to a known protein
(DNA affinity chromatography) or proteins bound to known
sequences (gel mobility shift)