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PDBsum entry 153d
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PDB id:
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DNA
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Title:
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Crystal structure of a mispaired dodecamer, d(cgagaattc(o6me)gcg)2, containing a carcinogenic o6-methylguanine
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Structure:
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DNA (5'-d( Cp Gp Ap Gp Ap Ap Tp Tp Cp (6Og)p 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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S.L.Ginell,J.Vojtechovsky,B.Gaffney,R.Jones,H.M.Berman
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Key ref:
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S.L.Ginell
et al.
(1994).
Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine.
Biochemistry,
33,
3487-3493.
PubMed id:
DOI:
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Date:
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16-Dec-93
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Release date:
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15-Jan-94
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Headers
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References
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C-G-A-G-A-A-T-T-C-6OG-C-G
12 bases
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C-G-A-G-A-A-T-T-C-6OG-C-G
12 bases
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DOI no:
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Biochemistry
33:3487-3493
(1994)
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PubMed id:
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Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine.
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S.L.Ginell,
J.Vojtechovsky,
B.Gaffney,
R.Jones,
H.M.Berman.
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ABSTRACT
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The crystal structure of the synthetic deoxydodecamer d(CGAGAATTC(O6Me)GCG)2 has
been determined and refined to an R-factor of 16.9% with data up to 2.9-A
resolution. This sequence contains two mismatched base pairs between
O6-methylguanine and adenine with the arrangement A(syn).(O6-Me)G(anti) which
differs from the geometry observed in solution by NMR. The intermolecular
arrangement is equivalent to the other isomorphous deoxydodecamers. However, the
weakening of some significant crystal packing contacts was observed and related
to the effect of stacking between the mispaired adenine and the adjacent guanine
in the sequence. The structure is highly hydrated, with a total of 49 solvent
molecules located. The methyl group and the mismatched base-pair geometry
locally disrupt the B-DNA-type solvent network with two solvent molecules found
close to the N1 and N6 of the mispaired adenine.
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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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A.Dimitri,
J.A.Burns,
S.Broyde,
and
D.A.Scicchitano
(2008).
Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
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Nucleic Acids Res,
36,
6459-6471.
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M.L.Coté,
S.J.Yohannan,
and
M.M.Georgiadis
(2000).
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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Acta Crystallogr D Biol Crystallogr,
56,
1120-1131.
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PDB code:
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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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B.Hartmann,
and
R.Lavery
(1996).
DNA structural forms.
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Q Rev Biophys,
29,
309-368.
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M.C.Wahl,
and
M.Sundaralingam
(1995).
New crystal structures of nucleic acids and their complexes.
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Curr Opin Struct Biol,
5,
282-295.
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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
