228
R.B. Stockbridge et al. / Bioorganic Chemistry 38 (2010) 224–228
Table 2
Activation parameters and rate constants for adenosine glycosidic bond cleavage compared to the enzyme-catalyzed reaction.
D
Gà
D
Hà
TD
Sà
t1/2 (yrs)
knon
kcat
kcat/knon
Adenosine
20-Deoxy-adenosine [20]
32.9 0.3
30.9
28.0
27.1
ꢁ4.9
ꢁ3.8
6000
180
3.7 ( 1.3) ꢀ 10ꢁ12 sꢁ1
18 sꢁ1a
0.2 sꢁ1b
4.9 ꢀ 1012
1.2 ꢀ 10ꢁ10 sꢁ1
2.8 ꢀ 108c
a
b
c
kcat value for Trypanosome brucei nucleoside ribohydrolase [6].
kcat value for adenine mismatch specific glycosylase MutY from E. coli [23]. Data obtained at 37 °C.
Rate enhancement calculated from rate constants at 37 °C.
the observed UV spectra are not consistent with a composite reac-
tion to which the base-catalyzed reaction contributes significantly.
Third, the base-catalyzed reaction yields a number of products that
can be observed in the 1H NMR spectrum including N6-ribosyl
derivatives of adenine and triaminopyrimidine. These products
were not observed for the reaction at pH 7, which also tends to
suggest that the rate constants measured at pH 7 are for a third,
uncatalyzed, reaction rather than for the combined acid- and
base-catalyzed reactions.
to be estimated. The reported rate constants are 30 sꢁ1 for ricin
A-chain [19] and 18 sꢁ1 for Trypanosome brucei nucleoside ribohy-
drolase [6]. Thus, the rate enhancement produced by both enzymes
is ꢂ5 ꢀ 1012, and these enzymes are among the more proficient
hydrolases that have been described [8].
It is also of interest to compare the rate enhancements gener-
ated by enzymes that catalyze adenosine and deoxyadenosine
hydrolysis at neutral pH. Uncatalyzed adenosine hydrolysis pro-
ceeds at a rate that is ꢂ30-fold slower than that previously re-
ported for deoxyadenosine hydrolysis [20]. (That effect of the
20 OH group on uncatalyzed glycosidic bond hydrolysis is some-
what less than the 650-fold effect that it exerts on acid-
catalyzed glycosidic bond cleavage [21].) Since many DNA glyco-
sylases exhibit rate constants below 1 sꢁ1 [20], these enzymes
are less proficient than enzymes involved in adenosine glycosidic
bond cleavage (Table 2). A quick turnover is probably less impor-
tant for enzymes involved in editing functions such as DNA exci-
sion and repair.
4.2. Mechanism of adenosine decomposition at pH 7
At pH 7, the adenine b-ribofuranoside starting material can
decompose by two principal pathways. In the first, adenosine
undergoes simple glycosidic bond hydrolysis to yield adenine and
ribose. The present results indicate that glycosidic bond cleavage
proceeds through an acid- and base-independent mechanism that
does not involve opening the adenine ring. Alternatively, the ribose
ring could open and re-close, yielding any of the other adenosine
anomers: the
Opening of the ribose ring was not observed in acid or base. To
our knowledge, this is the first time that the -furanoside and a-
a-furanoside, and the a- and b-pyranosides (Fig. 5).
Acknowledgments
a
We thank Laura Hall for performing preliminary HPLC separa-
tions of the adenosine anomers. This work was supported by NIH
grant GM-18325.
pyranoside have been obtained by the thermal degradation of ade-
nine b-ribofuranoside. Since it is likely that the open ribose ring
also re-closes to form the b-furanoside starting material, it is not
possible to determine the rate of ribose ring-opening from these
experiments. However, the sum of the rate constants of formation
of the other three anomers is similar in magnitude to the rate con-
stants of adenine formation, so it appears that ribose ring-opening
and glycosidic bond hydrolysis occur at similar rates.
References
[1] C. Romier, K. Reuter, D. Suck, R. Ficner, Biochemistry 35 (1996) 15734–15739.
[2] D.W. Parkin, B.A. Horenstein, D.R. Abdulah, B. Estupinan, V.L. Schramm, J. Biol.
Chem. 31 (1991) 20658–20665.
[3] B. Jung, M. Florchinger, H.H. Kunz, M. Traub, R. Wartenberg, W. Jeblick, H.E.
Neuhaus, T. Mohlmann, Plant Cell 21 (2009) 876–891.
[4] B.A. Horesnstein, D.W. Parkin, B. Estupinan, V.L. Schramm, Biochemistry 30
(1991) 10788–10795.
[5] B. Giabbai, M. Degano, Structure 12 (2004) 739–749.
[6] D.W. Parkin, J. Biol. Chem. 271 (1996) 21713–21719.
[7] Y. Endo, K. Mitsui, K. Motizuki, K. Tsurugi, J. Biol. Chem. 262 (1987)
5908–5912.
[8] R. Wolfenden, Chem. Rev. 106 (2006) 3379–3396.
[9] V.L. Schramm, Nucleic Acids Res. Suppl. 3 (2003) 107–108.
[10] S. Kim, R.B. Martin, Inorg. Chim. Acta 91 (1984) 19–24.
[11] D.W. Parkin, H.B. Leung, V.L. Schramm, J. Biol. Chem. 259 (1984) 9411–
9417.
[12] X.Y. Chen, P.J. Berti, V.L. Schramm, J. Am. Chem. Soc. 122 (2000) 1609–1617.
[13] E.R. Garrett, P.J. Mehta, J. Am. Chem. Soc. 94 (1972) 8532–8541.
[14] E.R. Garrett, P.J. Mehta, J. Am. Chem. Soc. 94 (1972) 8542–8547.
[15] P. Lehikoinen, J. Mattinen, H. Lonnberg, J. Org. Chem. 51 (1986) 3819–3823.
[16] K. Marat, Spinworks, Version 2.5.2, University of Manitoba, Winnipeg, MB,
1999–2007.
[17] C. Altona, M. Sundaralingam, J. Am. Chem. Soc. 95 (1973) 2333–2344.
[18] G. Kotowycz, R.U. Lemieux, Chem. Rev. 73 (1973) 669–698.
[19] Y. Endo, K. Tsurugi, J. Biol. Chem. 263 (1988) 8735–8739.
[20] G.K. Schroeder, R. Wolfenden, Biochemistry 46 (2007) 13638–13647.
[21] H.Z. Venner, Physiol. Chem. 339 (1964) 14–27.
Further kinetic analysis will be required to resolve the detailed
mechanism of adenosine decomposition at pH 7. It seems probable
that both glycosidic bond hydrolysis and anomerization involve
the development of positive charge at the anomeric carbon. Such
charge development is consistent with the small increase in rate
produced by an increase in ionic strength. A carbocation at C10
and coplanar intermediate would be required to allow rotation of
H10 and the adenine moiety to form the
a-adenosine anomers
(Fig. 5). For glycosidic bond cleavage, a buildup of positive charge
on C10 has been predicted for the enzymatic glycosidic bond cleav-
ages catalyzed by trypanosomal nucleoside hydrolase [4] and ricin
A-chain (for which a carbocation intermediate bearing a full charge
was proposed, [12]) on the basis of kinetic isotope effects on C10. It
seems likely that the neutral reaction would behave similarly,
although the details of proton transfer from water to adenine are
not clear at this time.
4.3. Rate enhancements generated by nucleoside hydrolases
[22] P. Ciuffreda, S. Casati, A. Manzocchi, Magn. Reson. Chem. 45 (2007) 781–
784.
[23] D.M. Noll, A. Gogos, J.A. Granek, N.D. Clarke, Biochemistry 38 (1999) 6374–
6379.
Comparison of rate constants observed for enzyme-catalyzed
and uncatalyzed reactions allows the rate enhancement, kcat/knon
,