Molecular structure of cyclic deoxydiadenylic acid at atomic resolution

Journal Article · Tue Nov 01 04:00:00 EST 1988 · Biochemistry; (United States)

DOI:https://doi.org/10.1021/bi00422a010· OSTI ID:6400077

Frederick, C A; Coll, M; van der Marel, G A; van Boom, J H; Wang, A H.J.

The molecular structure of a small cycle nucleotide, cyclic deoxydiadenylic acid, has been determined by single-crystal X-ray diffraction analysis and refined to an R factor of 7.8% at 1.0-/Angstrom/ resolution. The crystals are in the monoclinic space group C2 with unit cell dimensions of a = 24.511 (3) /Angstrom/, b = 24.785 (3) /Angstrom/, c = 13.743 (3) /Angstrom/, and ..beta.. = 94.02 (2)/degrees/. The structure was solved by the direct methods program SHELXS-86. There are 2 independent cyclic d(ApAp) molecules, 2 hydrated magnesium ions, and 26 water molecules in the asymmetric unit of the unit cell. The two cyclic d(ApAp) molecules have similar conformations within their 12-membered sugar-phosphate backbone ring, but they have quite different appearances due to the different glycosyl torsion angles that make one molecule more compact and the other extended and open. Three of the four deoxyribose rings are in the less common C3'-endo conformation. All four phosphate groups have their phosphodiester torsion angles ..cap alpha..//zeta/ in the gauche(+)/gauche(+) conformation. One of the cyclic d(ApAp) molecules associated with another symmetry-related molecule to form a self-intercalated dimer that is a stable structure in solution, as observed in NMR studies. Many interesting intermolecular interactions, including base-base stacking, ribose-base stacking, base pairing, base-phosphate hydrogen bonding, and metal ion-phosphate interactions, are found in the crystal lattice. This structure may be relevant for understanding the conformational potentiality of an endogenous biological regulator of cellulose synthesis, cyclic (GpGp).

• Research Organization: Massachusetts Institute of Technology, Cambridge (USA)
• OSTI ID: 6400077
• Journal Information: Biochemistry; (United States), Journal Name: Biochemistry; (United States) Vol. 27:22; ISSN BICHA
• Country of Publication: United States
• Language: English

Related Subjects

550602* -- Medicine-- External Radiation in Diagnostics-- (1980-)
62 RADIOLOGY AND NUCLEAR MEDICINE
COHERENT SCATTERING
CRYSTALLOGRAPHY
DIFFRACTION
MAGNETIC RESONANCE
MOLECULAR STRUCTURE
NUCLEAR MAGNETIC RESONANCE
NUCLEOTIDES
ORGANIC COMPOUNDS
RESONANCE
SCATTERING
STEREOCHEMISTRY
X-RAY DIFFRACTION