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Multinuclear Zn sites:
alkaline Phosphatase.
A.-F. Miller, 2008, pg
1
Structural Zn: Zn fingers
The most common Zn-binding motif in the human genome is
the so-called Zn-finger.
Zn2+ binds tightly with Td coordination, Kd ≈ 10-9-10-11M.
Binding is specific for Zn: 103 - 105 times more tighter Zn
binding than binding of the next tightest binders: Co2+, Fe2+
and Ni2+.
Protein folding is dependent on Zn2+ binding. The Zn finger
module has a minute hydrophobic core that is not sufficient to
stabilize the folded state in the absence of Zn. However
when Zn is bound, the protein structure can withstand boiling.
Consensus sequence is
(Tyr/Phe)-X-Cys-X2,4-Cys-X3-Phe-X5-Leu-X2-His-X3,4-His-X2-6
A.-F. Miller, 2008, pg
2
Zn fingers bind DNA and RNA
Zn coordination is via 2 His and 2 Cys in the first class of Zn
fingers discovered (C2H2 fingers)
C2C2 versions also exist, as do C6 di-Zn2+-binding proteins.
Zn fingers are usually modules of larger proteins. Proteins with
as many as 37 Zn fingers are known.
Their role is to bind specific sequences of DNA or RNA.
A number of Zn fingers occur in tandem in a protein. Each
finger recognizes 3 consecutive base pairs, so a string of Zn
fingers can selectively bind a unique sequence of DNA. The
other modules of the protein are thus targeted to a DNA
sequence where they may recruit RNA polymerase and thus
increase expression of down-stream genes.
A.-F. Miller, 2008, pg
3
Zn finger functions
Zinc finger-containing proteins participate in DNA replication
and repair, transcription and translation. Thus they coordinate
metabolism, signaling, cell proliferation and apoptosis.
HIV Zn fingers aid in binding and packaging viral RNA into new
virions. They also play a role in reverse transcription
Artificial zinc finger transcription factors have been used to
target specific DNA sequence, in combination with activation or
repression domains to switch genes on or off.
Upon depletion of Zn2+, non-specific interactions between Znfinger proteins and other domains and proteins can result.
A.-F. Miller, 2008, pg
4
Zn fingers
Zn stabilizing a very
small globular
structure with
almost no
hydrophobic core,
thus enabling these
DNA-binding
domains to be tiny
yet stable.
A ‘core’ of two side chains.
A.-F. Miller, 2008, pg
5
1p47.pdb E.PEISACH, C.O.PABO (2003) J.MOL.BIOL. 330:1
Zn fingers
Coordination to Zn
holds together separate
elements of structure.
N and C termini face
opposite sides: a string
of these units will be
extended.
A.-F. Miller, 2008, pg
6
1p47.pdb E.PEISACH, C.O.PABO (2003) J.MOL.BIOL. 330:1
Zn fingers
α helix lies in major groove
A.-F. Miller, 2008, pg
7
1p47.pdb E.PEISACH, C.O.PABO (2003) J.MOL.BIOL. 330:1
Zn fingers
Symmetry: helices in close,
sheets on outside.
A.-F. Miller, 2008, pg
8
1p47.pdb E.PEISACH, C.O.PABO (2003) J.MOL.BIOL. 330:1
Zn fingers
Amino acids projecting
our of α helix stick
into major groove and
contact edges of base
pairs (outside edges).
Binds to DNA to
regulate transcription of
5S rRNA.
Also binds to 5S RNA
stabilizing it and
escorting it to cytoplasm.
A.-F. Miller, 2008, pg
9
1p47.pdb E.PEISACH, C.O.PABO (2003) J.MOL.BIOL. 330:1
Sample problems
Metal ion and oxidation state
d-electron count.
High spin vs. low spin electronic configuration in Oh and Td
coordination.
Identities of coordinating amino acids, and modes of binding.
Hard-soft series and ligand-metal preferred pairing.
General schemes for metal acquisition.
Non-redox cations Na+, K+, Ca2+, Mg2+. Forms in which they
occur, roles they play, issues they raise. Why ?
Zn2+, the ‘simple’ transition metal ion: what does it do ? Why ?
A.-F. Miller, 2008, pg
10
Example
Uranyl ion (UO22+) is commonly used to form heavy-atom
derivatives for X-ray diffraction studies. Given that this is a
relatively hard ion, what sorts of functional groups would
you expect to be derivatized ?
How does this behaviour compare with that expected for
another heavy-metal derivatizing ion, Hg2+ ?
A.-F. Miller, 2008, pg
11