 |
PDBsum entry 160d
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
High resolution crystal structure of the a-Dna decamer d(cccggccggg). Novel intermolecular base-Paired g(G.C) triplets.
|
|
|
Authors
|
|
B.Ramakrishnan,
M.Sundaralingam.
|
|
|
Ref.
|
|
J Mol Biol, 1993,
231,
431-444.
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The DNA decamer d(CCCGGCCGGG) crystallizes in the orthorhombic space group
P2(1)2(1)2(1) with a = 24.88, b = 44.60 and c = 46.97 A containing a duplex in
the asymmetric unit. The structure was solved by molecular replacement and
refined to an R factor of 18.5% using 6033 reflections at 1.65 A resolution. The
decamer duplex adopts an A-DNA conformation. The abrupt dislocation of the
duplex at the fourth base-pair G(4).C(17) by an abutting symmetry related
molecule results in distortion of the backbone bonds of the fifth residue G(5),
P-O(5')(alpha) and C(4')-C(5')(gamma), to the trans conformations from their
favored gauche- and gauche+ conformations, respectively. In this close encounter
the terminal G(10).C(11) base-pair of the symmetry related molecule hydrogen
bonds to the G(4).C(17) base-pair forming a novel base-paired G(4)*(G10).C(11))
triplet, where G(4) is hydrogen bonded to both G(10) and C(11). To facilitate
this hydrogen bonding the G(4).C(17) base-pair slides into the minor groove,
causing a toll on the backbone conformation of the adjacent residue G(5). A
similar triplet base-pairing interaction with somewhat weaker hydrogen bonds
occurs at the pseudo dyad related C(7).G(14) base-pair with G(20) of another
symmetry related duplex. This pseudo triplet interaction (C(7).G(14))*G(20),
does not perturb the backgone alpha and gamma torsions of G(15). Both the novel
base triplets are non-planar. The abrupt dislocation/bend at the G(4).C(17)
base-pair jolts the global helical base-pair parameters, inclination, tilt,
roll, tip, etc. quite markedly. Therefore a better description of the helix
parameters is obtained by splitting the duplex and calculating the local helix
axis for the top half consisting of the first three base-pairs, and the lower
half consisting of the last six base-pairs, omitting the fourth base-pair. The
two half duplexes are bent by only 10 degrees. This structure further
demonstrates that crystal packing interactions, which can also be governed by
base sequence, play a dominant role in determining DNA conformation.
|
|
|
|
|
|
|
|
Headers
|
|
|
|
|
|
