Chemistry Reference
In-Depth Information
nucleophile and substrate specifi city. If all, or the majority of, the catalytically essen-
tial residues are carboxylates, with at least one invariable Asp, and if the enzyme
exhibits stricter catalytic specifi city than binding specifi city, catalysis almost cer-
tainly depends on two metal ions. Structure-specifi c FEN-1 and XPF endonucle-
ases,
120,121
RNase III and dicer endonucleases,
97,122
and Group II ribozymes catalysing
RNA splicing with high substrate specifi city, clearly fulfi l the criteria for a two-
metal-ion catalysis. A noted variation of two-metal-ion catalysis is the three metal
ions found in homodimeric LAGLIDADG homing endonucleases,
123
where a single
metal ion B is shared between two neighbouring active sites. Nevertheless, each
phosphoryl transfer reaction requires two metal ions coordinated by a conserved
Asp.
15.5 Concluding Remarks
In this chapter we have summarized the following properties of two-metal-ion
catalysis: (i) participation of the two metal ions in substrate recognition; (ii) the role
of metal ions, particularly at the B site, in destabilizing the enzyme-substrate complex
and driving the reaction forward; (iii) dependence on a specifi c electrostatic envi-
ronment rather than metal ion A per se for the nucleophile formation and nucle-
ophilic attack; (iv) movement of two metal ions towards each other to stabilize
transition state and facilitate product formation; (v) movement of two metal ions
away from each other to release products.
The key to two-metal-ion catalysis is the proper alignment of the metal ions
with regard to the catalytic residues and the nucleic acid substrate. The extensive
involvement of the nucleic acid substrate in metal-ion binding and the sensitivity of
metal ions to the coordination environment enable nucleic acid enzymes that utilize
two-metal-ion catalysis to convert small thermodynamic differences into large
changes in catalytic rate and achieve extraordinary specifi city.
Acknowledgements
I thank Dr R. Craigie for reviewing the manuscript and the Intramural Research
Program of the NIH, NIDDK for funding the research. Figures 15.1A, 15.5 and 15.7
are reproductions from
Mol. Cell
,
22
, 5 - 13 Figures 2 A, 1 B and 3 C, respectively.
References
1.
Jager , J. ; Pata , J.D.; Getting a grip: polymerases and their substrate complexes;
Curr.
Opin. Struct. Biol.
, 1999 ,
9
, 21 - 28 .
Armache , K.J. ; Kettenberger , H. ; Cramer , P. ; The dynamic machinery of mRNA elonga-
tion ;
Curr. Opin. Struct. Biol.
, 2005 ,
15
, 197 - 203 .
2.
