Chemistry Reference
In-Depth Information
RNase H
MutH
Figure 15.4
(Plate 16)
Two families of nucleases that have been shown to use two-metal-ion
catalysis: (A) RNase H is a prototype of the superfamily, which includes nucleases, retroviral
integrases, RuvC Holliday junction resolvase and dicer argonaute. The two catalytically essen-
tial Asps are located on two adjacent parallel strands (highlighted in cyan). Two additional
carboxylates may be required for catalysis. Two Mg
2+
are jointly coordinated by the carboxy-
lates and the scissile phosphate; (B) MutH represents another superfamily, which includes
type IIP restriction endonucleases, T7 endonuclease I (a Holliday junction resolvasae) and T4
exonuclease I. The catalytic residues, Asp (D), Glu (E) and Lys (K) are located on the diverg-
ing point of a
b
-hairpin (highlighted in cyan). The loop that contains the fi rst Asp, which plays
the central role in Mg
2+
coordination, is often disordered in the MutH-family nucleases in
the absence of a properly aligned substrate or divalent cations. A diagram of the metal ion
coordination in each case is shown below the actual structure (See colour plate section)
on the diverging point of a b - hairpin (Figure 15.4 B). The single conserved Asp
residue is located on the fi rst strand of the hairpin. This strand is fl exible and often
disordered in the crystal structures. The remaining Glu-X-Lys (X is a hydrophobic
residue) located on the second strand (Figure 15.4B) are not absolutely conserved.
The Glu is occasionally substituted by Gln, and Lys by Glu or Gln.
67
It has long been debated whether one, two or three metal ions are required for
the phosphoryl transfer reaction catalysed by RNase H- and MutH-like nucleases
and transposases. Disagreements typically stem from two general observations.
Firstly, among the high-resolution structures of apo-RNase H, transposase and ret-
roviral integrase, one or two metal binding sites have been identifi ed and the loca-
tions of metal ions vary from structure to structure.
68 - 71
Secondly, even in the presence
