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PDBsum entry 1n4l
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Transferase/DNA
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PDB id
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1n4l
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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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Staying straight with a-Tracts: a DNA analog of the HIV-1 polypurine tract.
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Authors
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M.L.Coté,
M.Pflomm,
M.M.Georgiadis.
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Ref.
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J Mol Biol, 2003,
330,
57-74.
[DOI no: ]
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PubMed id
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Abstract
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The polypurine tract (PPT) from the HIV-1 genome is resistant to digestion by
reverse transcriptase following (-)-strand synthesis and is used to prime
(+)-strand synthesis during retroviral replication. We have determined the
crystal structure of the asymmetric DNA/DNA analog16-mer duplex
(CTTTTTAAAAGAAAAG/CTTTTCTTTTAAAAAG) comprising most of the "visible"
portion of the RNA:DNA hybrid from the polypurine tract of HIV-1, which was
previously reported in a complex with HIV-1 reverse transcriptase. Our 16-mer
completely encompasses a 10-mer DNA duplex analog of the HIV-1 PPT. We report
here a detailed analysis of our B' form 16-mer DNA structure, including three
full pure A-tracts, as well as a comparative structural analysis with polypurine
tract and other A-tract-containing nucleic acid structures. Our analysis reveals
that the polypurine tract structures share structural features despite being
different nucleic acid forms (i.e. DNA:DNA versus RNA:DNA). In addition, the
previously reported A-tract-containing DNA molecules bound to topoisomerase I
are remarkably similar to our polypurine tract 16-mer structure. On the basis of
our analysis, we suggest that the specific topology of long pure A-tracts is
remarkably comparable across a wide array of biological environments.
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Figure 3.
Figure 3. View[41.] of the PPT DNA 16-mer of form IVc with
its numbering scheme. The asterisk (*) in the center indicates
where the crystallographic 2-fold rotation axis bisects the
non-self-complementary DNA. In this view the 2-fold axis is
neither identically parallel with nor perpendicular to the
viewer, hence the distorted asterisk for emphasis. Each model
used in structural refinement is a different color. The DNA is
self-complementary in its first five and last five base-pairs,
then there is a "type" similarity (pyrimidine/pyrimidine) in
step 6 (11), then the A versus T and T versus A differences of
the middle four base-pairs.
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Figure 8.
Figure 8. Difference electron density maps are shown
following refinement of only the protein, illustrating the
roadmap-like quality of the DNA density. The 2F[o] -F[c] map is
shown in green and contoured at 1.5s; the F[o] -F[c] map is
shown in white and contoured at 3.0s. The protein model is shown
with narrow stick figures, and the fitted DNA is shown with
thick stick figures.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2003,
330,
57-74)
copyright 2003.
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Secondary reference #1
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Title
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Crystal structures of an n-Terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-Primer binding to the fingers domain.
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Authors
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S.Najmudin,
M.L.Coté,
D.Sun,
S.Yohannan,
S.P.Montano,
J.Gu,
M.M.Georgiadis.
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Ref.
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J Mol Biol, 2000,
296,
613-632.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5. Superpositionings of the higher-resolution
structures at the DNA binding site. In both views the
backgrounded DNA molecule is that of form IV, and the ion-pair
formed between Asp114 and Arg116 in form IV is shown with black
dashes. Both views also show smaller bonds and atoms for the
dual conformations of Tyr64 of form IV. Superpositionings were
done using the same subset of alpha-carbon atoms listed for
Figure 2. (a) The superpositioning of the A and B protein
molecules of form I onto that of form IV. The main-chains and
side-chains nearly superimpose with the exception of the
main-chain of the form I B molecule in the region of Tyr64. (b)
Superpositioning of the A and B protein molecules of form IIa
onto that of form IV. The main and side-chain superpositionings
are nearly identical for the residues shown, and there is an
exact mapping of the Asp114 side-chain of the form IIa A
molecule and that of form IV.
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Figure 7.
Figure 7. Stereodiagrams of DNA bound to the fingers domain
of the MMLV RT fragment as modeled in the previously defined
binding cleft in HIV-1 RT. (a) A trace rendering shows the
fragment of MMLV RT in blue including the fingers and palm
domains superimposed on the fingers, palm, and thumb domains
from HIV-1 RT (2hmi structure) [Ding et al 1998]. DNA as bound
to the fingers domain in form IIb crystals is shown as a stick
model in red. The superpositioning of the fingers and palm
domains from MMLV RT and HIV-1 RT is based on the 160 most
similar residues as reported by [Georgiadis et al 1995] and
listed in the legend in Figure 2. (b) The same molecules are
superimposed as in (a). The DNA shown in red from the HIV-1
RT-DNA-Fab complex structure (2hmi) is shown for comparison in a
similar view along the cleft formed by the fingers, palm, and
thumb domains.
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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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Use of an n-Terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-Mer DNA molecule containing g-A mispairs.
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Authors
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M.L.Coté,
S.J.Yohannan,
M.M.Georgiadis.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2000,
56,
1120-1131.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5 Schematic representation (Kraulis, 1991[Kraulis, P. J.
(1991). J. Appl. Cryst. 24, 946-950.]; Merritt & Bacon,
1997[Merritt, E. A. & Bacon, D. J. (1997). Methods Enzymol. 277,
505-524.]) of the interactions in the protein-DNA binding site
of form IV. The hydrogen-bonding distances between 2.4 and 3.3
Å are indicated with white dotted lines. The non-bonded contacts
ranging from 3.3 to 3.7 Å are indicated with longer-dashed
magenta lines. Also shown with black dotted lines is the
ion-pair formed by D114 O  1
with R116 N  and
D114 O 2
and R116 N  2 as
observed in form IV.
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Figure 7.
Figure 7 The superpositioning (Jones et al., 1991[Jones, T. A.,
Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst.
A47, 110-119.]) of the observed pseudo-hexadecamer model
(containing the anti A7) onto a theoretical intact hexadecamer
containing bridging phosphate groups. (a) The navy-blue stick
model (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24,
946-950.]) depicts the observed pseudo-hexadecamer. The gold
stick model represents the intact hexadecamer model, with the
bridging phosphate groups emphasized in red. (b) A stereodiagram
(Merritt & Bacon, 1997[Merritt, E. A. & Bacon, D. J. (1997).
Methods Enzymol. 277, 505-524.]) close-up of the region where
the phosphate group would most likely occur in an intact
hexadecamer. The color schemes shown are identical to that in
(a). Clearly shown are the two chain termini in the navy-blue
model (the observed structure), the contiguous chain represented
by the intact gold model containing the red phosphate group and
the close agreement between the two.
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #3
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Title
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Structure of a pseudo-16-Mer DNA with stacked guanines and two g-A mispairs complexed with the n-Terminal fragment of moloney murine leukemia virus reverse transcriptase.
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Authors
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M.L.Coté,
M.M.Georgiadis.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
1238-1250.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4 Comparative views (Kraulis, 1991[Kraulis, P. J. (1991).
J. Appl. Cryst. 24, 946-950.]; Merritt & Bacon, 1997[Merritt, E.
A. & Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.]) of
the protein-DNA binding sites of the (a) form IVa and the (b)
form IVb structures. In each view, the characteristic ion-pair
between Asp114 and Arg116 is shown with black dotted lines.
Green dotted lines denote hydrogen bonds whose distances range
from 2.4 to 3.3 Å. Magenta dashed lines represent contacts
whose distances are greater than 3.3 Å and less than 3.8 Å.
Note the difference in the disposition of the Asp114-Arg116 ion
pair in its interaction with the nucleic acid in the form IVa
versus the IVb structure. Note the absence of contacts to the
DNA from Tyr64 in the form IVb structure.
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Figure 6.
Figure 6 Stereoview (Kraulis, 1991[Kraulis, P. J. (1991). J.
Appl. Cryst. 24, 946-950.]; Merritt & Bacon, 1997[Merritt, E. A.
& Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.]) of the
form IVa and form IVb pseudo-hexadecamers resulting from the
superpositioning of the C^  atoms
of the protein molecules of their structures. Note the
near-exact match of the 3'-OH ribose rings and the lack of
matches elsewhere. The form IVb DNA is shown in red and the form
IVa DNA is shown in white, retaining its A7 base in the anti
conformation.
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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