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PDBsum entry 1a84
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DOI no:
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Biochemistry
37:9230-9239
(1998)
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PubMed id:
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NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin.
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A.Gelasco,
S.J.Lippard.
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ABSTRACT
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The structure of the DNA duplex dodecamer, d(CCTCTGGTCTCC. GGAGACCAGAGG),
containing the cisplatin d(GpG) 1,2-intrastrand cross-link at the position
denoted by asterisks, was determined in solution by high-resolution 2D NMR
spectroscopy and restrained molecular dynamics refinement. The
cis-[Pt(NH3)2¿d(GpG-N7(1), N7(2))¿] lesion causes the adjacent guanine bases
to roll toward one another by 49 degrees, leading to an overall helix bend angle
of 78 degrees. These features are more exaggerated than those observed in the
X-ray crystal structure determined for the same platinated duplex [Takahara et
al. (1995) Nature 377, 649-652]. A common property of the solution and crystal
structures is the widening and flattening of the minor groove opposite the
platinum adduct, affording geometric parameters resembling those found in A-form
DNA. This deformation is especially noteworthy for the solution structure
because its sugar puckers are primarily those of B-form DNA. The unwinding of
the helix at the site of platination is 25 degrees. The curvature and shape of
the platinated duplex are remarkably similar to those observed in DNA duplexes
complexed by the HMG-domain proteins SRY and LEF-1. The structure reveals how
cisplatin binding alters DNA in such a manner as to facilitate HMG-domain
protein recognition.
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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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Structural basis for cisplatin DNA damage tolerance by human polymerase η during cancer chemotherapy.
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Nat Struct Mol Biol,
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PDB code:
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F.Zobi,
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Redox-induced binding of [(tacn)Re(II)Br(CO)2]+ to guanine, oligonucleotides, and peptides.
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PDB code:
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Chemistry,
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R.C.Todd,
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Metallomics,
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Nucleic Acids Res,
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Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex.
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Cell,
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PDB codes:
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J.A.Brown,
S.A.Newmister,
K.A.Fiala,
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Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase.
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Nucleic Acids Res,
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J Mol Model,
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F.Brueckner,
T.Carell,
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(2007).
Mechanism of transcriptional stalling at cisplatin-damaged DNA.
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Nat Struct Mol Biol,
14,
1127-1133.
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PDB code:
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M.Dal Peraro,
P.Ruggerone,
S.Raugei,
F.L.Gervasio,
and
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Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations.
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Curr Opin Struct Biol,
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M.Pavelka,
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Pt-bridges in various single-strand and double-helix DNA sequences. DFT and MP2 study of the cisplatin coordination with guanine, adenine, and cytosine.
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J Mol Model,
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Anal Bioanal Chem,
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S.Sharma,
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B.Temple,
D.Bhattacharyya,
N.V.Dokholyan,
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(2007).
Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics.
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J Mol Biol,
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Y.Wu,
D.Bhattacharyya,
C.L.King,
I.Baskerville-Abraham,
S.H.Huh,
G.Boysen,
J.A.Swenberg,
B.Temple,
S.L.Campbell,
and
S.G.Chaney
(2007).
Solution structures of a DNA dodecamer duplex with and without a cisplatin 1,2-d(GG) intrastrand cross-link: comparison with the same DNA duplex containing an oxaliplatin 1,2-d(GG) intrastrand cross-link.
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Biochemistry,
46,
6477-6487.
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PDB codes:
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F.R.Salsbury,
J.E.Clodfelter,
M.B.Gentry,
T.Hollis,
and
K.D.Scarpinato
(2006).
The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response.
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Nucleic Acids Res,
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I.Ott,
and
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[Special qualities of inorganic cytostatics. Medicinal chemistry of platinum complexes]
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Pharm Unserer Zeit,
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J.Vinje,
and
E.Sletten
(2006).
Internal versus terminal metalation of double-helical oligodeoxyribonucleotides.
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Chemistry,
12,
676-688.
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K.Spiegel,
and
A.Magistrato
(2006).
Modeling anticancer drug-DNA interactions via mixed QM/MM molecular dynamics simulations.
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Org Biomol Chem,
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S.Komeda,
J.M.Teuben,
M.A.Elizondo-Riojas,
J.Reedijk,
and
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(2006).
A pyrazolato-bridged dinuclear platinum(II) complex induces only minor distortions upon DNA-binding.
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Chemistry,
12,
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A.Sischka,
K.Toensing,
R.Eckel,
S.D.Wilking,
N.Sewald,
R.Ros,
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Molecular mechanisms and kinetics between DNA and DNA binding ligands.
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Biophys J,
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DDB1-DDB2 (xeroderma pigmentosum group E) protein complex recognizes a cyclobutane pyrimidine dimer, mismatches, apurinic/apyrimidinic sites, and compound lesions in DNA.
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J Biol Chem,
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Differential activation of DNA-PK based on DNA strand orientation and sequence bias.
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Nucleic Acids Res,
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O.Delalande,
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Chiral differentiation of DNA adducts formed by enantiomeric analogues of antitumor cisplatin is sequence-dependent.
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Biophys J,
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S.G.Chaney,
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E.Bassett,
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Recognition and processing of cisplatin- and oxaliplatin-DNA adducts.
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Crit Rev Oncol Hematol,
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I.Gómez-Pinto,
E.Cubero,
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V.Monaco,
G.van der Marel,
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M.Orozco,
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Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct.
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J Biol Chem,
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PDB codes:
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J.Kasparkova,
M.Fojta,
N.Farrell,
and
V.Brabec
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Differential recognition by the tumor suppressor protein p53 of DNA modified by the novel antitumor trinuclear platinum drug BBR3464 and cisplatin.
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Nucleic Acids Res,
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R.C.van Waardenburg,
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C.Verseyden,
D.Pluim,
L.E.Jansen,
M.A.Bjornsti,
and
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Platinated DNA adducts enhance poisoning of DNA topoisomerase I by camptothecin.
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J Biol Chem,
279,
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D.Tsankov,
B.Kalisch,
J.H.van de Sande,
and
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Cisplatin adducts of d(CCTCTG*G*TCTCC).d(GGAGACCAGAGG) in aqueous solution by vibrational circular dichroism spectroscopy.
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Biopolymers,
72,
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L.J.Ming
(2003).
Structure and function of "metalloantibiotics".
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Med Res Rev,
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T.Stevnsner,
C.Modin,
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Functional consequences of mutations in the conserved SF2 motifs and post-translational phosphorylation of the CSB protein.
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Nucleic Acids Res,
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A.M.Soto,
B.I.Kankia,
P.Dande,
B.Gold,
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Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA.
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Nucleic Acids Res,
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2.4-A crystal structure of the asymmetric platinum complex [Pt(ammine)(cyclohexylamine)]2+ bound to a dodecamer DNA duplex.
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J Biol Chem,
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PDB code:
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B.I.Kankia,
A.M.Soto,
N.Burns,
R.Shikiya,
C.S.Tung,
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V.Brabec,
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Molecular aspects of resistance to antitumor platinum drugs.
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Drug Resist Updat,
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C.Hofr,
N.Farrell,
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Thermodynamic properties of duplex DNA containing a site-specific d(GpG) intrastrand crosslink formed by an antitumor dinuclear platinum complex.
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Nucleic Acids Res,
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M.Stros
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Two mutations of basic residues within the N-terminus of HMG-1 B domain with different effects on DNA supercoiling and binding to bent DNA.
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Biochemistry,
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A.A.Travers,
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HMG-D complexed to a bulge DNA: an NMR model.
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Protein Sci,
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PDB code:
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T.Mizukoshi,
T.S.Kodama,
Y.Fujiwara,
T.Furuno,
M.Nakanishi,
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Structural study of DNA duplexes containing the (6-4) photoproduct by fluorescence resonance energy transfer.
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Nucleic Acids Res,
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Efficient translesion replication past oxaliplatin and cisplatin GpG adducts by human DNA polymerase eta.
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Biochemistry,
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A.Vaisman,
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The efficiency and fidelity of translesion synthesis past cisplatin and oxaliplatin GpG adducts by human DNA polymerase beta.
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J Biol Chem,
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H.Kostrhunova,
and
V.Brabec
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Conformational analysis of site-specific DNA cross-links of cisplatin-distamycin conjugates.
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Biochemistry,
39,
12639-12649.
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J.Malina,
C.Hofr,
L.Maresca,
G.Natile,
and
V.Brabec
(2000).
DNA interactions of antitumor cisplatin analogs containing enantiomeric amine ligands.
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Biophys J,
78,
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Q.He,
U.M.Ohndorf,
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(2000).
Intercalating residues determine the mode of HMG1 domains A and B binding to cisplatin-modified DNA.
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Biochemistry,
39,
14426-14435.
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R.M.Brosh,
J.K.Karow,
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I.D.Hickson,
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Potent inhibition of werner and bloom helicases by DNA minor groove binding drugs.
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Nucleic Acids Res,
28,
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C.M.Barnes,
C.S.Chow,
and
S.J.Lippard
(1999).
Structural and kinetic studies of a cisplatin-modified DNA icosamer binding to HMG1 domain B.
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J Biol Chem,
274,
12346-12354.
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H.Loskotová,
and
V.Brabec
(1999).
DNA interactions of cisplatin tethered to the DNA minor groove binder distamycin.
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Eur J Biochem,
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J.Reedijk
(1999).
Medicinal applications of heavy-metal compounds.
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Curr Opin Chem Biol,
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G.Zlokarnik,
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S.J.Lippard
(1999).
Rapid fluorescence-based reporter-gene assays to evaluate the cytotoxicity and antitumor drug potential of platinum complexes.
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| |
Chem Biol,
6,
541-551.
|
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Y.Fujiwara,
C.Masutani,
T.Mizukoshi,
J.Kondo,
F.Hanaoka,
and
S.Iwai
(1999).
Characterization of DNA recognition by the human UV-damaged DNA-binding protein.
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J Biol Chem,
274,
20027-20033.
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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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