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PDBsum entry 1ztt
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Transferase/DNA
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PDB id
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1ztt
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References listed in PDB file
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Key reference
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Title
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A host-Guest approach for determining drug-Dna interactions: an example using netropsin.
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Authors
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K.D.Goodwin,
E.C.Long,
M.M.Georgiadis.
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Ref.
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Nucleic Acids Res, 2005,
33,
4106-4116.
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PubMed id
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Abstract
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Netropsin is a well-characterized DNA minor groove binding compound that serves
as a model for the study of drug-DNA interactions. Our laboratory has developed
a novel host-guest approach to study drug-DNA interactions in which the host,
the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase
(MMLV RT) is co-crystallized with a DNA oligonucleotide guest in the presence
and absence of drug. We have co-crystallized netropsin with the RT fragment
bound to the symmetric 16mer d(CTTAATTCGAATTAAG)2 and determined the structure
of the complex at 1.85 A. In contrast to previously reported netropsin-DNA
structures, our oligonucleotide contains two AATT sites that bind netropsin with
flanking 5' and 3' sequences that are not symmetric. The asymmetric unit of the
RT fragment-DNA-netropsin crystals contains one protein molecule and one-half of
the 16mer with one netropsin molecule bound. The guanidinium moiety of netropsin
binds in a narrow part of the minor groove, while the amidinium is bound in the
widest region within the site. We compare this structure to other Class I
netropsin-DNA structures and find that the asymmetry of minor groove widths in
the AATT site contributes to the orientation of netropsin within the groove
while hydrogen bonding patterns vary in the different structures.
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Figure 1.
(A) The crystal structure of an RT fragment-DNA-netropsin complex. The
asymmetric unit consists of one protein molecule, an 8 bp oligonucleotide duplex and one
netropsin molecule representing half of the symmetric complex. The dashed vertical line
divides the symmetrically equivalent halves of the 16 bp oligonucleotide. The DNA
oligonucleotide is shown in a red sticks model, and netropsin is shown in a purple CPK
model. RT is shown as a ribbon rendering with ß-strands in green, coils in yellow and
{alpha} -helices in blue except for the {alpha} D helix in magenta. Residues
Tyr-64, Asp-114, Leu-115, Arg-116 and Gly-191 that make contacts with the DNA are shown in
black ball-and-sticks models. (B) Schematic of the oligonucleotide duplex with the two
complementary strands (B and G) and the numbering scheme referred to in the text. Arrows
denote netropsin molecules oriented from guanidinium (tail) to amidinium end (head).
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Figure 6.
(A) Minor groove widths of DNA base-pair steps (from 3DNA calculations) in the
absence (open circle) and presence (black diamond) of netropsin. (B) Stereo diagram of
structures of DNA in the absence (red) and presence (blue) of netropsin (r.m.s.d = 0.9 Å).
Superimpositioning of C1' of all 16 bp was done using O (19).
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