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PDBsum entry 1prp
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DOI no:
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Biochemistry
32:13838-13843
(1993)
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PubMed id:
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Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine.
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C.M.Nunn,
T.C.Jenkins,
S.Neidle.
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ABSTRACT
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The crystal structure of the complex between propamidine and the
self-complementary DNA dodecamer d(CGCGAATTCGCG) duplex has been determined to a
resolution of 2.1 A and a R-factor of 17.4%. The propamidine binds to the DNA
within the minor groove, with specific hydrogen-bonding interactions from the
amidinium groups to the bases and sugar groups of the DNA, via a 4-base-pair
binding site. A network of water molecules lies over the mouth of the minor
groove. The structure provides a rationale for the superior DNA-binding
properties of propamidine as compared to pentamidine [cf. Edwards, K. J.,
Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. This is seen
to result from (i) decreased minor groove width at the binding site and (ii)
reduced mobility of the bound propamidine molecule.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.Mitsuyama,
N.Nomura,
K.Hashimoto,
E.Yamada,
H.Nishikawa,
M.Kaeriyama,
A.Kimura,
Y.Todo,
and
H.Narita
(2008).
In vitro and in vivo antifungal activities of T-2307, a novel arylamidine.
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Antimicrob Agents Chemother,
52,
1318-1324.
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T.Sun,
and
Y.Zhang
(2008).
Pentamidine binds to tRNA through non-specific hydrophobic interactions and inhibits aminoacylation and translation.
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Nucleic Acids Res,
36,
1654-1664.
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X.Qu,
J.Ren,
P.V.Riccelli,
A.S.Benight,
and
J.B.Chaires
(2003).
Enthalpy/entropy compensation: influence of DNA flanking sequence on the binding of 7-amino actinomycin D to its primary binding site in short DNA duplexes.
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Biochemistry,
42,
11960-11967.
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K.Shi,
S.N.Mitra,
and
M.Sundaralingam
(2002).
Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin.
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Acta Crystallogr D Biol Crystallogr,
58,
601-606.
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PDB code:
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Y.Zhang,
Z.Li,
D.S.Pilch,
and
M.J.Leibowitz
(2002).
Pentamidine inhibits catalytic activity of group I intron Ca.LSU by altering RNA folding.
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Nucleic Acids Res,
30,
2961-2971.
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B.S.Reddy,
S.M.Sondhi,
and
J.W.Lown
(1999).
Synthetic DNA minor groove-binding drugs.
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Pharmacol Ther,
84,
1.
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A.Guerri,
I.J.Simpson,
and
S.Neidle
(1998).
Visualisation of extensive water ribbons and networks in a DNA minor-groove drug complex.
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Nucleic Acids Res,
26,
2873-2878.
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PDB code:
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G.R.Clark,
D.W.Boykin,
A.Czarny,
and
S.Neidle
(1997).
Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition.
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Nucleic Acids Res,
25,
1510-1515.
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PDB code:
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M.A.Young,
G.Ravishanker,
and
D.L.Beveridge
(1997).
A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation.
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Biophys J,
73,
2313-2336.
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D.Sengupta,
A.Blaskó,
and
T.C.Bruice
(1996).
A microgonotropen pentaaza pentabutylamine and its interactions with DNA.
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Bioorg Med Chem,
4,
803-813.
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G.R.Clark,
C.J.Squire,
E.J.Gray,
W.Leupin,
and
S.Neidle
(1996).
Designer DNA-binding drugs: the crystal structure of a meta-hydroxy analogue of Hoechst 33258 bound to d(CGCGAATTCGCG)2.
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Nucleic Acids Res,
24,
4882-4889.
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PDB codes:
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L.Tabernero,
J.Bella,
and
C.Alemán
(1996).
Hydrogen bond geometry in DNA-minor groove binding drug complexes.
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Nucleic Acids Res,
24,
3458-3466.
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C.Alhambra,
F.J.Luque,
J.Portugal,
and
M.Orozco
(1995).
Molecular dynamics study of the binding of elsamicin A to DNA.
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Eur J Biochem,
230,
555-566.
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M.A.Young,
G.Ravishanker,
D.L.Beveridge,
and
H.M.Berman
(1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
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Biophys J,
68,
2454-2468.
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M.R.Conte,
T.C.Jenkins,
and
A.N.Lane
(1995).
Interaction of minor-groove-binding diamidine ligands with an asymmetric DNA duplex. NMR and molecular modelling studies.
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Eur J Biochem,
229,
433-444.
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C.M.Nunn,
T.C.Jenkins,
and
S.Neidle
(1994).
Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition.
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Eur J Biochem,
226,
953-961.
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PDB code:
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E.Liepinsh,
W.Leupin,
and
G.Otting
(1994).
Hydration of DNA in aqueous solution: NMR evidence for a kinetic destabilization of the minor groove hydration of d-(TTAA)2 versus d-(AATT)2 segments.
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Nucleic Acids Res,
22,
2249-2254.
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I.Radhakrishnan,
and
D.J.Patel
(1994).
Hydration sites in purine.purine.pyrimidine and pyrimidine.purine.pyrimidine DNA triplexes in aqueous solution.
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Structure,
2,
395-405.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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