1dj6

From Proteopedia

---

Revision as of 01:03, 25 November 2007

proteopedia linkproteopedia link

spinqualitylabelsall models 1dj6, resolution 1.0Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

COMPLEX OF A Z-DNA HEXAMER, D(CG)3, WITH SYNTHETIC POLYAMINE AT ROOM TEMPERATURE

Overview

The crystal structure of a left-handed Z-DNA hexamer, d(CG)(3) in complex, with a synthetic polyamine, N(1)-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine, NH(3)(+)-(CH(2))(2)-NH(2)(+)-(CH(2))(2)-NH(2)(+)-(CH(2))(2)-NH(3)(+), [PA(222)], has been determined by the X-ray diffraction method at 1.0 A, resolution. In an orthorhombic crystal, the d(CG)(3) duplex binds two, PA(222) molecules, and this synthetic polyamine exhibits dual, conformational properties. One of the two PA(222) molecules resides on the, floor of the minor groove of a Z-DNA duplex and imino groups bridge the, two phosphate chains across a double helix, while the terminal amino, groups link the oxygen atoms O2 of four cytosine bases. This PA(222), molecule makes a U-turn like a fishhook at one of its ends to provide a, micro-environmental network previously unseen in complexes of DNA with, polyamines. The width of the minor groove does not become considerably, greater with the looped end of the polyamine, indicating conformational, rigidity of the Z-DNA backbone imposed by the high stacking energy of the, GC base pairs. While polyamine binding to the minor groove has been, postulated by theoretical studies for stabilizing the Z-DNA double helical, conformation, the finding in the crystal of the looped polyamine chain, binding the minor groove of Z-DNA is observed for the first time from the, data collected at 10 degrees C (so-called room temperature data). Another, PA(222) molecule binds on the convex outer surface of the major groove of, the Z-DNA duplex and links three d(CG)(3) duplexes which are symmetrically, related to each other. The structure of this PA(222) presents the, previously reported zig-zag type conformation [Egli et al., Biochemistry, 30 (1991) 11388-11402]. Comparison of this structure with other, polyamine-DNA cocrystals reveals structural themes and differences that, may relate to the length of the polyamine.

About this Structure

1DJ6 is a Protein complex structure of sequences from [1] with MG and 104 as ligands. Full crystallographic information is available from OCA.

Reference

The crystal structure of N(1)-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine (polyamines) binding to the minor groove of d(CGCGCG)(2), hexamer at room temperature., Ohishi H, Suzuki K, Ohtsuchi M, Hakoshima T, Rich A, FEBS Lett. 2002 Jul 17;523(1-3):29-34. PMID:12123799

Page seeded by OCA on Sun Nov 25 03:11:07 2007