540

Biochimica et Biophysica Acta,

563 ( 1 9 7 9 ) 540--544 © E l s e v i e r / N o r t h - H o l l a n d Biomedical Press

BBA Report BBA 91484

THE CRYSTAL AND MOLECULAR STRUCTURE OF 9-a-D-ARABINOFURANOSYLADENINE

S U S A N J. C L I N E a n d D E R E K J. H O D G S O N *

Department of Chemistry, University of North Carolina, Chapel Hill, NC 2 7514 (U.S.A.) (Received February 20th, 1979)

Key words: a-Arabinofuranosyladenine; a-Arabinonucleoside; Crystallography

Summary The glycosyl torsional angles in two crystallographically-independent molecules of a-araA are - 7 3 and - 6 4 °, both of which are in the " a n t i " region. The sugar conformations are C (3')-endo and C (2')-exo-C (3')-endo. In order for most of the nucleosides of purines and their analogs to be biologically active, t h e y must be converted to nucleotides; the principal enzyme responsible for their phosphorylation in mammalian cells is adenosine kinase. Bennett and Hill [1 ] have noted that the only requirement for the nucleoside or its analog to act as a substrate is that the 2'-hydroxy group be trans to the purine. Hence, adenosine (I), 8-azaadenosine, 9-a-D-arabinofuranosyl-8-azaadenine, and 9-a-D-arabinofuranosyladenine (a-araA) (II) are HOH2C

O

Adenine

HOH2C

O

HOH2C HO

HO

OH

(I)

HO

O

Adenine

Adenine HO

n

OH

m

*To w h o m correspondence should be addressed.

Abbreviation: ~-axaA, 9-~-D=arabinofuranosyladenine. Supplementary data to this article are deposited with, and can be obtained from, Elsevier/NorthHolland Biomedical Press, BBA Data Deposition, P.O. Box 1345, 1000 BH Amsterdam, The Netherlands. Reference should be made to No. BBA/DD/107191484/563(1979) 540. The supplementary information includes: positional parameters and observed and calculated structure amplitudes (electrons X 10) for ~-araA; b o n d lengths (A) and b o n d angles (o) in ~-araA and ~-araA.

541 active, while the analogs 9-~-D-ribofuranosyladenine (a-adenosine) (TIT) and 9-/3-D-arabinoribofuranosyl-8-azaadenine are inactive [1 ]. The current research activity in the biochemistry of the arabinonucleosides and a-nucleosides leads naturally to a need to determine the structures of these species, and several structural studies of arabinonucleosides have been reported [ 2--11 ]. The structures of the ~-nucleosides have also been extensively studied [ 12-20], although of the reported structures only one is of an anomer of a major nucleic acid constituent (~-cytidine, Ref. 20). To our knowledge, however, no structural study of an ~-arabinonucleoside has been reported to date; we here report the structural and conformational properties of such a nucleoside, 9-~-D-arabinofuranosyladenine, ~-araA. A sample of ~-araA was generously donated by Dr. J.A. Montgomery, and colorless crystals were obtained with great difficulty from alcoholic medium. The nucleoside crystallizes in the non-centrosymmetric orthorhombic space group P212121 with eight molecules in a cell of dimensions a = 6.720(5), b = 40.188(35), and c = 8.357(8) £ . A total of 1173 data greater than 3a was collected using an automatic diffractometer equipped with CuK~ radiation and a nickel filter. The structure was solved using the direct methods program MULTAN [21]. The positional and anisotropic thermal parameters

N(6)

C(6) N(I)(

pN(7)

~-/C (8) N(9)

N(5)

C(I I ) 0(41 ) O(

C(4 t)

C(3~)i o(3f)(

tC(5 I)

Fig. 1. V i e w o f o n e m o l e c u l e o f 9 - ~ - D - a r a b i n o f u r a n o s y l a d e n i n e . H y d r o g e n a t o m s are o m i t t e d f o r c l a r • . i J i t y . T h e m o l e c u l e s h o w n is m o l e c u l e A , w h o s e sugar c o n f o r m a t i o n is C ( 2 ) - e x o - C ( 3 )-endo.

542 of all non-hydrogen atoms have been refined b y full-matrix least-squares techniques. All but one of the 26 hydrogen atoms were included but not refined; these hydrogen atoms were placed in calculated positions when possible, while the remainder were located in the Fourier map. The final R-factor (on F) is 0.076. A view of the nucleoside is shown in Fig. 1. The atomic coordinates of ~-araA and the bond lengths and angles in ~-araA and ~-araA are deposited in the BBA Data Bank. The glycosyl torsional angle, ×, is defined [22] as the dihedral angle C(8) -N( 9 ) -C( 1' ) -O (4'); this angle is positive if there is clockwise rotation of the N(9)-C(8) bond relative to the O(4')-C(1') bond as viewed along the C(I')-N(9) bond, and zero if the N(9)-C(8) and O(4')-C(1') bonds are cisplanar. As was originally noted by D o n o h u e and Trueblood [23], the probable ranges for × in ~-nucleosides are - 1 5 ° to +75 ° (anti) and 165 ° to 255 ° (syn). The × values o f - 6 4 ( 2 ) ° and - 7 3 ( 2 ) ° obtained in the t w o independent molecules of ~-araA are in the anti-region (for the ~-anomer) and are virtually in the range o f - 3 0 ° to - 7 2 ° noted by Sundaralingam [24] in an early summary of ~-nucleoside structures. Moreover, these values can be compared with those of +57.8 ° and +29.7 ° observed for ~-araA [2] and its cation [3], respectively. It is apparent that the present structure exhibits a glycosyl torsion which is roughly enantiomeric to that in its ~-anomer. As can be seen from Fig. 1, the conformation around the extracyclic C(4')-C(5') bond is the c o m m o n gauche-gauche in both independent molecules. This is, however, in contrast to the gauche-trans conformation observed for b o t h adenosine [25] and araA [2]. One sugar (A) exhibits the C(2')-exo-C(3')endo, 2T 3 conformation which is c o m m o n l y observed in ~-nucleosides [24], with C(2') lying 0.50 • below the three-atom plane and C(3') lying 0.30 A above it. The other molecule (B) shows the C(3')-endo, 3E conformation, with C(3') 0.58 A above the four-atom plane. This latter conformation is unc o m m o n in ~-nucleosides, although it does occur in the ~-nucleotide vitamin B-12 c o e n z y m e [26]. The sugar torsional angles are listed in Table I. The interplanar angles between the least-squares planes through the base and the sugar atoms C(I'), C(4'), 0 ( 4 ' ) are 99 ° and 101 ° in the t w o independent molecules. There is extensive hydrogen bonding in the structure. Both molecules exhibit the N(6)-H--. N(7) intermolecular hydrogen bond which is c o m m o n l y observed in adenine derivatives [ 27 ], with N(6)... N(7) distances and N(6)-H.--N(7) angles of 3.28(1), 3.01(1) A and 158 and 150 ° in the A and B molecules, respectively. In addition, the molecules are linked in the crystal b y 0 ( 3 ' ) A . . . 0 ( 5 ' ) A , 0 ( 2 ' ) B . . . N ( 3 ) A , and 0 ( 3 ' ) B " .0(2')A intermolecular hydrogen bonds. TABLE I S U G A R T O R S I O N A L A N G L E S IN c~-amA Molecule

Puckering

% 0(4')-C(1' )

~rz C(1')-C(2')

1"2 C(2')-C(3')

r~ C(3')-C(4')

r4 C(4')-0(4')

A B

C(2')-exo-C(8')-endo C(8')-endo

20 0

--48 --24

48

--38

37

--36

11 24

543 As in most nucleoside structures [28], there is some base stacking in the crystals of ~-araA, although considerably less than is found in some other structures. In the present structure, as is shown in Fig. 2, there is some overlap between the imidazole moiety of molecule A and the pyrimidine ring of a screw-related molecule B. The molecular planes are not exactly parallel, but are inclined at an angle of 15.75 °. The average interplanar separation is 3.19 A. Although the × torsional angle in ~-araA is much closer to that observed in ~-araA than that in adenosine, it is necessarily true that the 2'-group and the purine in ~-araA do exist in approximately the same spatial relationship (i.e. trans) as the corresponding groups in the crystals of adenosine; this observation is, of course, entirely consistent with the suggestion of Bennett and Hill [ 1 ] that active substrates of adenosine kinase must be able to adopt the same conformation as the enzyme-bound form of adenosine. Indeed, the conformation observed here for ~-araA is very similar to that depicted by Bennett and Hill (see Ref. 1, Fig. 1B) for the 8-aza analog of ~-araA. Thus, while the present experiment cannot show that ~-araA adopts an analogous conformation to that of adenosine in the enzyme-bound form, it does provide apodictic evidence that such a conformation is possible. We are grateful to Dr. J.A. Montgomery for providing the sample and to Mr. Eric Steen for growing the crystal used in this study.

Fig. 2. V i e w o f the stacking arrangement in ~-araA. T h e heavily shaded ( t o p ) m o l e c u l e is m o l e c u l e A.

544

References 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28

Bennett~ L.L., Jr. and Hill, D.L. (1975) Mol. Pharmacol. 11, 803--808 Bunick, G. and Voet, D. (1974) Acta Crystallogr. B30, 1 651--1660 Chwang, A.K., Sundaralingam, M. and Hanessian, S. (1974) Acta Crystallogr. B30, 2273--2277 Chwang, A.K. and SundaraUngam, M. (1973) Nature New Biol. 243, 78--80; Tougard, P. and Lefebvre-Soubeyran, O. (1974) Acta Crystallogr. B30, 76--89 Sherfinski, J. and Marsh, R. (1973) Aeta Crystallogr. B29, 192--198 Birnbaum, G.I., Darzynkiewicz, E. and Shugar, D. (1975) J. Am. Chem. Soe. 97, 5904--5908 Kung, W., Marsh, R.E. and Kainosho, M. (1977) J. Am. Chem. Soc. 99, 5471--5477 ToUin, P., Wilson, H.R. and Young, D.W. (1973) Acta Crystallogr. B29, 1641--1647 Saenger, W. (1972) J. Am. Chem. Soc. 94, 621---626 Tougard, P. (1973) Bioehim. Biophys. Acta 319, 116--121 Tougard, P. (1973) Acta Crystallogr. B29, 2227--2232 Shefter, E., Kotick, M.P. and Bardos, T.J. (1967) J. Pharm. Sci. 56, 1293--1299 Frank, G.W. (1968) Am. Cryst. Assoc. S u m m e r Meeting, Paper L3 Rohrer, D.C. and Sundaralingam, M. (1970) J. Am. Chem. SDe. 92, 4 9 5 0 - - 4 9 5 5 Rohrer, D.C. and Sundaralingam, M. (1970) J. Am. Chem. Soc. 92, 4 9 5 6 - - 4 9 6 2 Gutowski, G.E., Chaney, M.O., Jones, N.D., Hamill, R.L., Davis, F.A. and Miller, R.D. (1973) Biochem. Biophys. Res. Commun. 5 1 , 3 1 2 - - 3 1 7 Lee, K.C. and Kartha, G. (1974) Am. Cryst. Assoc. S u m m e r Meeting, Paper $1 Birnbaum, G.I., Giziewicz, J., Huber, C.P. and Shugar, D. (1976) J. Am. Chem. Soc. 98, 4640-4644 Armstrong, V.W., Dattagupta, J.K., Eckstein, F. and Saenger, W. (1976) Nucl. Acids Res. 3, 1791-1810 Post, M.L., Birnbaum, G.I., Huber, C.P. and Shugar, D. (1977) Biochim. Biophys. A c t a 479, 133-142 Main, P., Woolfson, M.M. and Germain, G. (1971) MULTAN: A C o m p u t e r Program for the A u t o m a t i c So lution of Crystal Structures, University of Y ork Sundaralingam, M. (1969) Biopolymers 7, 821--860 Donohue, J. and Trueblood, K.N. (1960) J. Mol. Biol. 2, 363--371 Sundaralingam, M. (1971) J. Am. Chem. Soc. 93, 6644---6647 Lai, T.F. and Marsh, R.E. (1972) Acta Crystallogr. B28, 1982--1989 Lenhert, P.G. (1968) Proc. Roy. Soc., Ser. A, 303, 45--83 Singh, P. and Hodgson, D.J. (1979) Acta Crystallogr., B 3 5 , 9 7 3 - - 9 7 6 Bugg, C.E. (1972) in The Purines, Theory and E x p e r i m e n t (Bergmann, E.D. and Pullman, B., eds.), pp. 178--204, Israel Academy of Sciences and Humanities

The crystal and molecular structure of 9-alpha-D-arabinofuranosyladenine.

540 Biochimica et Biophysica Acta, 563 ( 1 9 7 9 ) 540--544 © E l s e v i e r / N o r t h - H o l l a n d Biomedical Press BBA Report BBA 91484 TH...
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