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PDBsum entry 1jb7
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DNA-binding protein/DNA
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PDB id
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1jb7
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Dna g-Quartets in a 1.86 a resolution structure of an oxytricha nova telomeric protein-Dna complex.
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Authors
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M.P.Horvath,
S.C.Schultz.
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Ref.
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J Mol Biol, 2001,
310,
367-377.
[DOI no: ]
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PubMed id
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Abstract
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The Oxytricha nova telomere end binding protein (OnTEBP) recognizes, binds and
protects the single-stranded 3'-terminal DNA extension found at the ends of
macronuclear chromosomes. The structure of this complex shows that the single
strand GGGGTTTTGGGG DNA binds in a deep cleft between the two protein subunits
of OnTEBP, adopting a non-helical and irregular conformation. In extending the
resolution limit of this structure to 1.86 A, we were surprised to find a
G-quartet linked dimer of the GGGGTTTTGGGG DNA also packing within the crystal
lattice and interacting with the telomere end binding protein. The G-quartet DNA
exhibits the same structure and topology as previously observed in solution by
NMR with diagonally crossing d(TTTT) loops at either end of the four-stranded
helix. Additionally, the crystal structure reveals clearly visible Na(+), and
specific patterns of bound water molecules in the four non-equivalent grooves.
Although the G-quartet:protein contact surfaces are modest and might simply
represent crystal packing interactions, it is interesting to speculate that the
two types of telomeric DNA-protein interactions observed here might both be
important in telomere biology.
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Figure 4.
Figure 4. Hydration of the G-quartet linked G[4]T[4]G[4] DNA
dimer. Electron density maps and schematic representations are
shown side-by-side for water molecules bound in the four
grooves. The electron density map is colored gray for the DNA
grooves and blue for the water molecules. In the schematic
phosphorous atoms are colored yellow, non-bridging phosphate
oxygen atoms are red, N2 (and N3 if shown) atoms are green, the
C8 atom is gray, water molecules are cyan for 1–2 σ peaks in
the S.A. omit electron density maps and dark blue for>2 σ
peaks. The deoxyribose group is a pentagon and the bases are
represented as rectangles. The position in the 5′ → 3′
sequence and the syn/anti conformation about the N-glycosyl bond
of each base is indicated. From top to bottom the grooves are
the (a) wide groove (10 Å across), (b) intermediate I (4.6
Å across), (c) narrow (3.0 Å across), and (d)
intermediate II (4.6 Å across). The two intermediate
grooves and associated hydration patterns are pseudo 2-fold
symmetric, so each DNA-water interaction is corroborated by two
independent observations. In solution, the wide and narrow
grooves are each pseudo 2-fold symmetric, but water interactions
are not exactly repeated in the top and bottom halves of these
two grooves presumably because of protein and lattice
interactions.
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Figure 5.
Figure 5. Distribution of waters interacting with N3, N2,
and C8 groups of the G bases. (a) All 16 G-G base-pairs are
superimposed and shown as a generalized G-G pair. The number of
observations for each hydration site is indicated. (b) The
N2-water-O4' bridge and the C8-water-OP bridge are shown for the
anti-anti G-G configuration. (c) The N2-water-OP bridge and (d)
the C8-water-O4' bridge are other examples of bidentate water
interactions and each of these bridges involves a base in the
syn conformation.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
310,
367-377)
copyright 2001.
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Secondary reference #1
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Title
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Crystal structure of the oxytricha nova telomere end binding protein complexed with single strand DNA.
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Authors
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M.P.Horvath,
V.L.Schweiker,
J.M.Bevilacqua,
J.A.Ruggles,
S.C.Schultz.
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Ref.
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Cell, 1998,
95,
963-974.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. Oligonucleotide/Oligosaccharide–Binding (OB)
Folds within On TEBPThe four OB folds of On TEBP are shown in
the top row. Residue limits for each OB fold of On TEBP are
indicated and the labels are colored as in Figure 1: light
purple and dark purple for the two OB folds of the α N-terminal
domain, green for the α C-terminal domain, and blue for β. The
OB folds from the α N-terminal domain and β subunit each
interact with the single strand telomeric DNA, shown as a gray
stick model. The OB fold from the α C-terminal domain is shown
complexed with the extended peptide loop of the β subunit,
shown as a blue stick model. For comparison, the originally
described ( [32]) examples of the OB fold are shown in the
bottom row. These are the B subunit of verotoxin-1 from E. coli,
the anticodon-binding domain of aspartyl-tRNA synthetase
complexed with tRNA, staphylococcal nuclease complexed with the
Ca^2+-pTp inhibitor, and fd gene V protein. The strands and
loops of the OB fold are colored as follows: strand S1 in blue;
strand S2 in cyan; strand S3 in yellow; loop L[3–4] and the
intervening helix H, if present, in green; strand S4 in orange;
and strand S5 in red.
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Figure 3.
Figure 3. Protein–Protein Interactions in On TEBP(A)
Surface representation of the protein–protein association. α
is shown as a solvent-accessible surfaceβ is shown as an
α-carbon trace in blue, and the ssDNA is shown as a ribbon with
boxes for the base groups (yellow, G; blue, T). A large groove
that associates with helix C[β] of β is apparent, as are the
surfaces that interact with the extended peptide loop of β. Two
leucine residues at the surface of α that interact with the
N-terminal portion of helix C[β] are indicated by the colored
patches on α, with purple showing the location of L236[α] and
green showing the location of L330[α]. Three residues at the
C-terminal region of helix C[β] form a hydrophobic ridge, and
these are shown in blue. From the middle of helix C[β] to the
C-terminal end these residues are L156[β], I160[β], and
V164[β].(B) Detailed view of the residues at the
protein–protein interface. Notice how helix C[β] of β (blue)
bridges the N-terminal (purple) and C-terminal (green) domains
of α. The peptide loop of β follows directly after the last
turn of this helix (residue V164[β]). Hydrophobic side chains
(gray) close to the surface of the α C-terminal domain create
two hydrophobic patches that align with clusters of hydrophobic
residues located along this extended peptide loop of β.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Refined solution structure of the dimeric quadruplex formed from the oxytricha telomeric oligonucleotide d(ggggttttgggg).
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Authors
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P.Schultze,
F.W.Smith,
J.Feigon.
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Ref.
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Structure, 1994,
2,
221-233.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Stereoviews of the eight Oxy-1.5 structures with the
lowest total energies out of a set of 20 calculations. (a) view
into one of the medium grooves and (b) view into narrow groove,
which is parallel to the two-fold rotation axis of symmetry. In
one strand, guanines are red and thymines are orange; in the
other strand, guanines are green and thymines are yellow. The
red 5′ end is in front, close to the yellow thymine loop. The
green 5′ end is at the back, next to the orange loop.
Figure 1. Stereoviews of the eight Oxy-1.5 structures with the
lowest total energies out of a set of 20 calculations. (a) view
into one of the medium grooves and (b) view into narrow groove,
which is parallel to the two-fold rotation axis of symmetry. In
one strand, guanines are red and thymines are orange; in the
other strand, guanines are green and thymines are yellow. The
red 5′ end is in front, close to the yellow thymine loop. The
green 5′ end is at the back, next to the orange loop.
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Figure 6.
Figure 6. Comparison of the refined three-dimensional
structures of Oxy-1.5. (a) Solution NMR structure and (b) X-ray
crystal structure ([28], Brookhaven Protein Data Base entry
1D59). The color scheme is the same as Figure 1. The solution
structure shown is a stereo- view of the lowest energy structure
of the eight refined structures. The X-ray structure is a
stereoview from coordinates of one of the two
crystallographically distinct models. Figure 6. Comparison
of the refined three-dimensional structures of Oxy-1.5. (a)
Solution NMR structure and (b) X-ray crystal structure ([[4]28],
Brookhaven Protein Data Base entry 1D59). The color scheme is
the same as [5]Figure 1. The solution structure shown is a
stereo- view of the lowest energy structure of the eight refined
structures. The X-ray structure is a stereoview from coordinates
of one of the two crystallographically distinct models.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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