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PDBsum entry 1ncs
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Transcription regulation
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PDB id
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1ncs
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References listed in PDB file
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Key reference
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Title
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The solution structure of the first zinc finger domain of swi5: a novel structural extension to a common fold.
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Authors
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R.N.Dutnall,
D.Neuhaus,
D.Rhodes.
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Ref.
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Structure, 1996,
4,
599-611.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
96%.
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Abstract
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BACKGROUND: The 2Cys-2His (C2-H2) zinc finger is a protein domain commonly used
for sequence-specific DNA recognition. The zinc fingers of the yeast
transcription factors SWI5 and ACE2 share strong sequence homology, which
extends into a region N-terminal to the first finger, suggesting that the
DNA-binding domains of these two proteins include additional structural
elements. RESULTS: Structural analysis of the zinc fingers of SWI5 reveals that
a 15 residue region N-terminal to the finger motifs forms part of the structure
of the first finger domain, adding a beta strand and a helix not previously
observed in other zinc finger structures. Sequence analysis suggests that other
zinc finger proteins may also have this structure. Biochemical studies show that
this additional structure increases DNA-binding affinity. CONCLUSIONS: The
structural analysis presented reveals a novel zinc finger structure in which
additional structural elements have been added to the C2-H2 zinc finger fold.
This additional structure may enhance stability and has implications for DNA
recognition by extending the potential DNA-binding surface of a single zinc
finger domain.
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Figure 5.
Figure 5. Stereo view of backbone N, Cα, C atom trace of the
lowest energy structure of peptide m30F. The Cα atom of every
fifth residue is shown as a black sphere and the backbone N
atoms of slowly exchanging NH groups are shown in cyan. The side
chain heavy atoms of the zinc ligands are coloured as in Figure
4a. Figure 5. Stereo view of backbone N, Cα, C atom trace
of the lowest energy structure of peptide m30F. The Cα atom of
every fifth residue is shown as a black sphere and the backbone
N atoms of slowly exchanging NH groups are shown in cyan. The
side chain heavy atoms of the zinc ligands are coloured as in
[3]Figure 4a.
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Figure 8.
Figure 8. Model of the first zinc finger of SWI5 docked to
B-form DNA. A schematic representation of the zinc finger
structure is shown prepared as in Figure 4a. The sequence of the
DNA is that of the primary binding site of SWI5 and the two
DNA-strands are coloured differently for contrast. The protein N
and C termini and zinc ion are marked as well as the 5′ and
3′ ends of the DNA strand (dark blue) to which the additional
helix makes its closest approach. The DNA-recognition helix of
the canonical zinc finger is positioned to contact a base
triplet on the cyan strand. This arrangement positions the
additional helix near the opposite (dark blue) strand across the
major groove, at a suitable distance (≈7 å) for basic
residues on the surface of the helix to reach phosphate groups
of the DNA backbone. Figure 8. Model of the first zinc
finger of SWI5 docked to B-form DNA. A schematic representation
of the zinc finger structure is shown prepared as in [3]Figure
4a. The sequence of the DNA is that of the primary binding site
of SWI5 and the two DNA-strands are coloured differently for
contrast. The protein N and C termini and zinc ion are marked as
well as the 5′ and 3′ ends of the DNA strand (dark blue) to
which the additional helix makes its closest approach. The
DNA-recognition helix of the canonical zinc finger is positioned
to contact a base triplet on the cyan strand. This arrangement
positions the additional helix near the opposite (dark blue)
strand across the major groove, at a suitable distance (≈7
å) for basic residues on the surface of the helix to reach
phosphate groups of the DNA backbone.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(1996,
4,
599-611)
copyright 1996.
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Secondary reference #1
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Title
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Adjacent zinc-Finger motifs in multiple zinc-Finger peptides from swi5 form structurally independent, Flexibly linked domains.
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Authors
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Y.Nakaseko,
D.Neuhaus,
A.Klug,
D.Rhodes.
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Ref.
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J Mol Biol, 1992,
228,
619-636.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Sequence specific bining of isolated SW15
peptides containing two and three zinc-finger motifs from
WI5. The autoradiograph shows DNase I footprints of
the two-finger peptide mlOFS and the three-finger peptide
lOFST. The two-finger peptide occupies about 213 of the
inding site of the thre-finger peptide, starting at the 5'
end. The t of the three-finger peptide is very
similar to tht of intact WIS, and is located in the
romoter region o the HO gene at locations - 1290 to
- 1308 from the start of he gene (Stillman et al., 1988).
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Figure 8.
rg30 8.03 383 1.6%1.83$
er3 1 7.58 414 379-385
is32 750 427 303, 314
le33 8.65 347 2.07
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Solution structures of two zinc-Finger domains from swi5 obtained using two-Dimensional 1h nuclear magnetic resonance spectroscopy. A zinc-Finger structure with a third strand of beta-Sheet.
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Authors
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D.Neuhaus,
Y.Nakaseko,
J.W.Schwabe,
A.Klug.
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Ref.
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J Mol Biol, 1992,
228,
637-651.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5. Schematic representation of the structures of ingers 1 panels and B) and 2 (panels C and D) from SW15,
prepared using the program Molscript (Kraulis, 1991). In each case, the structure having the lowest NOE violations is
shown. iews A and C are related to views B and D by a 90'' rotation bout the vertical. In addition to the schematic
representtion of the backbone, bonds are shown between the non-hydrogen atoms of the side-chains of the metal
binding an conserved hydrophobic residues, nd these rsidues are labelled (not that, because the arrows representing
the /3sheet do not necessarily pass through the actual c'' atom positions, the C''-CB bonds of some side-chains have been
extended with broken lines so as to meet the bacbone representation artificially).
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Figure 6.
Figure 6. Stereoview of a local ackbone superimposition in the turn regio (Cvs44 to Cys49) between the two
P-strands of fingr 2 of SWIS; as in Fig. 3,45 structures are shown. Atoms Nj: NH, C'', e and 0' re shown for all residues,
tog&her with the zinc ions and he non-hydrogen side-chain atoms of Cys44, Pro47 and Cys49. The conformation is
clearly that of tpe II p-turn, characterized by the hydrogen bond between His46 C = 0 and Cys49 ?u'H (indicated hy
the broken line) and by the relative orientation of the Pro47-Gly48 peptide bond.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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