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PDBsum entry 1lov
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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A nucleophile activation dyad in ribonucleases. A combined X-Ray crystallographic/ab initio quantum chemical study.
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Authors
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P.Mignon,
J.Steyaert,
R.Loris,
P.Geerlings,
S.Loverix.
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Ref.
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J Biol Chem, 2002,
277,
36770-36774.
[DOI no: ]
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PubMed id
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Abstract
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Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in RNA
up to 10(15)-fold, as compared with the uncatalyzed reaction. High resolution
crystal structures of these enzymes in complex with 3'-mononucleotide substrates
demonstrate the accommodation of the nucleophilic 2'-OH group in a binding
pocket comprising the catalytic base (glutamate or histidine) and a charged
hydrogen bond donor (lysine or histidine). Ab initio quantum chemical
calculations performed on such Michaelis complexes of the mammalian RNase A (EC
) and the microbial RNase T(1) (EC ) show negative charge build up on the
2'-oxygen upon substrate binding. The increased nucleophilicity results from
stronger hydrogen bonding to the catalytic base, which is mediated by a hydrogen
bond from the charged donor. This hitherto unrecognized catalytic dyad in
ribonucleases constitutes a general mechanism for nucleophile activation in both
enzymic and RNA-catalyzed phosphoryl transfer reactions.
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Figure 1.
Fig. 1. Classical acid/base mechanism for RNase-catalyzed
phosphoryl transfer reactions. AH and B represent the catalytic
acid and base respectively; bent arrows represent the movement
of electrons.
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Figure 3.
Fig. 3. Correlation between the Mulliken charge on the
nucleophilic oxygen atom and the experimentally observed second
order rate constant (36) for the attack of phenolate,
p-cyanophenolate, p-chlorophenolate and p-ethoxycarboxyphenolate
on methyl 2,4-dinitrophenyl phosphate (n = 4, R2 = 0.9844).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
36770-36774)
copyright 2002.
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