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PDBsum entry 2dbe
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PDB id:
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DNA
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Title:
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Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding
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Structure:
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DNA (5'-d( Cp Gp Cp Gp Ap Ap Tp Tp Cp Gp Cp G)-3'). Chain: a, b. Engineered: yes
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Source:
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Synthetic: yes
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Biol. unit:
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Dimer (from
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Resolution:
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Authors:
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D.G.Brown,M.R.Sanderson,J.V.Skelly,T.C.Jenkins,T.Brown,E.Garman, D.I.Stuart,S.Neidle
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Key ref:
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D.G.Brown
et al.
(1990).
Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding.
Embo J,
9,
1329-1334.
PubMed id:
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Date:
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19-Mar-90
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Release date:
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15-Jul-91
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Headers
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References
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C-G-C-G-A-A-T-T-C-G-C-G
12 bases
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C-G-C-G-A-A-T-T-C-G-C-G
12 bases
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Embo J
9:1329-1334
(1990)
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PubMed id:
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Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding.
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D.G.Brown,
M.R.Sanderson,
J.V.Skelly,
T.C.Jenkins,
T.Brown,
E.Garman,
D.I.Stuart,
S.Neidle.
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ABSTRACT
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The three-dimensional structure of a complex between the dodecanucleotide
d(CGCGAATTCGCG) and the anti-trypanocidal drug berenil, has been determined to a
resolution of 2.5 A. The structure has been solved by molecular replacement and
refined to an R factor of 0.177. A total of 49 water molecules have been
located. The drug is bound at the 5'-AAT-3' region of the oligonucleotide. At
one end of the drug the amidinium group is in hydrogen-bonded contact with N3 of
the adenine base complementary to the thymine of the AAT. The other amidinium
group does not make direct interactions with the DNA. Instead, a water molecule
mediates between them. This is in hydrogen-bonded contact with an amidinium
nitrogen atom, N3 of the 5' end adenine base and the ring oxygen atom of an
adjacent deoxyribose. Molecular mechanics calculations have been performed on
this complex, with the drug at various positions along the sequence. These show
that the observed position is only 0.8 kcal/mol higher in energy than the best
position. It is suggested that there is a broad energy well in the AATT region
for this drug, and that water molecules as well as the neighbouring sequence,
will determine precise positioning. More general aspects of minor groove binding
are discussed.
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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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C.Caramelo-Nunes,
T.Tente,
P.Almeida,
J.C.Marcos,
and
C.T.Tomaz
(2011).
Specific berenil-DNA interactions: an approach for separation of plasmid isoforms by pseudo-affinity chromatography.
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Anal Biochem,
412,
153-158.
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B.Nguyen,
S.Neidle,
and
W.D.Wilson
(2009).
A role for water molecules in DNA-ligand minor groove recognition.
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Acc Chem Res,
42,
11-21.
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B.Nguyen,
and
W.D.Wilson
(2009).
The effects of hairpin loops on ligand-DNA interactions.
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J Phys Chem B,
113,
14329-14335.
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W.D.Wilson,
F.A.Tanious,
A.Mathis,
D.Tevis,
J.E.Hall,
and
D.W.Boykin
(2008).
Antiparasitic compounds that target DNA.
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Biochimie,
90,
999.
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M.Munde,
M.Lee,
S.Neidle,
R.Arafa,
D.W.Boykin,
Y.Liu,
C.Bailly,
and
W.D.Wilson
(2007).
Induced fit conformational changes of a "reversed amidine" heterocycle: optimized interactions in a DNA minor groove complex.
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J Am Chem Soc,
129,
5688-5698.
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PDB code:
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A.Adams,
C.Leong,
W.A.Denny,
and
J.M.Guss
(2005).
Structures of two minor-groove-binding quinolinium quaternary salts complexed with d(CGCGAATTCGCG)(2) at 1.6 and 1.8 Angstrom resolution.
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Acta Crystallogr D Biol Crystallogr,
61,
1348-1353.
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PDB codes:
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B.Nguyen,
D.Hamelberg,
C.Bailly,
P.Colson,
J.Stanek,
R.Brun,
S.Neidle,
and
W.D.Wilson
(2004).
Characterization of a novel DNA minor-groove complex.
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Biophys J,
86,
1028-1041.
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A.Madhumalar,
and
M.Bansal
(2003).
Structural insights into the effect of hydration and ions on A-tract DNA: a molecular dynamics study.
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Biophys J,
85,
1805-1816.
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C.Bailly,
G.Chessari,
C.Carrasco,
A.Joubert,
J.Mann,
W.D.Wilson,
and
S.Neidle
(2003).
Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition.
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Nucleic Acids Res,
31,
1514-1524.
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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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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.F.Bonifacio,
T.Brown,
G.L.Conn,
and
A.N.Lane
(1997).
Comparison of the electrophoretic and hydrodynamic properties of DNA and RNA oligonucleotide duplexes.
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Biophys J,
73,
1532-1538.
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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.J.Waring,
and
C.Bailly
(1997).
The influence of the exocyclic amino group characteristic of GC base pairs on molecular recognition of specific nucleotide sequences in DNA by berenil and DAPI.
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J Mol Recognit,
10,
121-127.
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P.Arlotta,
A.Rustighi,
F.Mantovani,
G.Manfioletti,
V.Giancotti,
G.Tell,
and
G.Damante
(1997).
High mobility group I proteins interfere with the homeodomains binding to DNA.
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J Biol Chem,
272,
29904-29910.
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C.A.Laughton,
F.Tanious,
C.M.Nunn,
D.W.Boykin,
W.D.Wilson,
and
S.Neidle
(1996).
A crystallographic and spectroscopic study of the complex between d(CGCGAATTCGCG)2 and 2,5-bis(4-guanylphenyl)furan, an analogue of berenil. Structural origins of enhanced DNA-binding affinity.
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Biochemistry,
35,
5655-5661.
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PDB code:
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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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G.R.Clark,
E.J.Gray,
S.Neidle,
Y.H.Li,
and
W.Leupin
(1996).
Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex.
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Biochemistry,
35,
13745-13752.
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PDB code:
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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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M.Durand,
and
J.C.Maurizot
(1996).
Distamycin A complexation with a nucleic acid triple helix.
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Biochemistry,
35,
9133-9139.
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A.A.Wood,
C.M.Nunn,
A.Czarny,
D.W.Boykin,
and
S.Neidle
(1995).
Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2.
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Nucleic Acids Res,
23,
3678-3684.
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PDB code:
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A.Abu-Daya,
P.M.Brown,
and
K.R.Fox
(1995).
DNA sequence preferences of several AT-selective minor groove binding ligands.
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Nucleic Acids Res,
23,
3385-3392.
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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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N.Spink,
D.G.Brown,
J.V.Skelly,
and
S.Neidle
(1994).
Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex.
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Nucleic Acids Res,
22,
1607-1612.
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PDB code:
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T.C.Jenkins,
A.N.Lane,
S.Neidle,
and
D.G.Brown
(1993).
NMR and molecular modeling studies of the interaction of berenil and pentamidine with d(CGCAAATTTGCG)2.
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Eur J Biochem,
213,
1175-1184.
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A.Dorn,
M.Affolter,
M.Müller,
W.J.Gehring,
and
W.Leupin
(1992).
Distamycin-induced inhibition of homeodomain-DNA complexes.
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EMBO J,
11,
279-286.
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C.Bailly,
J.P.Hénichart,
P.Colson,
and
C.Houssier
(1992).
Drug-DNA sequence-dependent interactions analysed by electric linear dichroism.
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J Mol Recognit,
5,
155-171.
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S.H.Hu,
K.Weisz,
T.L.James,
and
R.H.Shafer
(1992).
H-NMR studies on d(GCTTAAGC)2 and its complex with berenil.
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Eur J Biochem,
204,
31-38.
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C.A.Laughton,
T.C.Jenkins,
K.R.Fox,
and
S.Neidle
(1990).
Interaction of berenil with the tyrT DNA sequence studied by footprinting and molecular modelling. Implications for the design of sequence-specific DNA recognition agents.
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Nucleic Acids Res,
18,
4479-4488.
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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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Links
