1D16

STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS

Summary for 1D16

• Entry DOI: 10.2210/pdb1d16/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*CP*GP*TP*TP*TP*TP*CP*GP*CP*GP*CP*G)-3') (2 entities in total)
• Functional Keywords: z-dna stem, single strand, hairpin loop, dna
• Total number of polymer chains: 1
• Total formula weight: 4882.14

Authors

Chattopadhyaya, R.,Grzeskowiak, K.,Dickerson, R.E. (deposition date: 1988-04-12, release date: 1989-01-09, Last modification date: 2024-02-07)

Primary citation

Chattopadhyaya, R.,Grzeskowiak, K.,Dickerson, R.E.
Structure of a T4 hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops.
J.Mol.Biol., 211:189-210, 1990

PubMed Abstract: The synthetic DNA oligomer C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G crystallizes as a Z-DNA hexamer, capped at one end by a T4 loop. The crystals are monoclinic, space group C2, with a = 57.18 A, b = 21.63 A, c = 36.40 A, beta = 95.22 degrees, and one hairpin molecule per asymmetric unit. The structure of the z-hexamer stem was determined by molecular replacement, and the T4 loop was positioned by difference map methods. The final R factor at 2.1 A resolution for hairpin plus 70 water molecules is 20% for 2 sigma data, with a root-mean-square error of 0.26 A. The (C-G)3 stem resembles the free Z-DNA hexamer with minor crystal packing effects. The T4 loop differs from that observed on a B-DNA stem in solution, or in longer loops in tRNA, in that it shows intraloop and intermolecular interactions rather than base stacking on the final base-pair of the stem. Bases T7, T8 and T9 stack with one another and with the sugar of T7. Two T10 bases from different molecules stack between the C1-G12 terminal base-pairs of a third and fourth molecule, to simulate a T.T "base-pair". Distances between thymine N and O atoms suggest that the two thymine bases are hydrogen bonded, and a keto-enol tautomer pair is favored over disordered keto-keto wobble pairs. The hairpin molecules pack in the crystal in herringbone columns in a manner that accounts well for the observed relative crystal growth rates in a, b and c directions. Hydration seems to be most extensive around the phosphate groups, with lesser hydration within the grooves.

PubMed: 2299669
DOI: 10.1016/0022-2836(90)90020-M

Experimental method

X-RAY DIFFRACTION (2.1 Å)