336D

INTERACTION BETWEEN LEFT-HANDED Z-DNA AND POLYAMINE-3 THE CRYSTAL STRUCTURE OF THE D(CG)3 AND THERMOSPERMINE COMPLEX

Summary for 336D

• Entry DOI: 10.2210/pdb336d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'), N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: z-dna, double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 4073.70

Authors

Ohishi, H.,Terasoma, N.,Nakanishi, I.,Van Der Marel, G.,Van Boom, J.H.,Rich, A.,Wang, A.H.-J.,Hakoshima, T.,Tomita, K.-I. (deposition date: 1997-06-24, release date: 1998-04-10, Last modification date: 2024-02-21)

Primary citation

Ohishi, H.,Terasoma, N.,Nakanishi, I.,van der Marel, G.,van Boom, J.H.,Rich, A.,Wang, A.H.,Hakoshima, T.,Tomita, K.
Interaction between left-handed Z-DNA and polyamine - 3. The crystal structure of the d(CG)3 and thermospermine complex.
FEBS Lett., 398:291-296, 1996

PubMed Abstract: The DNA fragment, d(CG)3, was co-crystallized with N-(3-amino-propyl)-N-(5-aminopropyl)-l,4 -diaminobutane (thermospermine; PA(334)), a polyamine metabolized from the nucleic acid. By using a good crystal with dimensions of 0.5 x 0.5 x 0.5 mm3, X-ray intensity data were collected up to 1.0 A resolution. Two thermospermine molecules and a magnesium cation were bound to the left-handed double-helical d(CG)3 molecule. The d(CG)3 molecule adopted the left-handed Z-conformation and two thermospermine molecules and a magnesium cation neutralized the negative charges of the phosphate groups of the d(CG)3 molecule. Furthermore, the binding modes between d(CG)3 and thermospermine were different from those of d(CG)3 complexes with PA(24), spermidine and spermine. This is the first case in which it was determined by X-ray crystallographic analysis that one of two thermospermine molecules bound three d(CG)3 duplexes which were symmetrically related to each other, and the other formed two hydrogen bonds at the N(5) and N(9) atoms with two adjacent nucleotide phosphate groups of a single d(CG)3 strand at the minor groove. Furthermore, no direct coordination bond was found between the d(CG)3 molecule and the magnesium cation.

PubMed: 8977125
DOI: 10.1016/S0014-5793(96)01225-2

Experimental method

X-RAY DIFFRACTION (1 Å)