Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Nov;15(11):1228-31.
doi: 10.1038/nsmb.1502. Epub 2008 Oct 26.

An equivalent metal ion in one- and two-metal-ion catalysis

Wei Yang  1
Affiliations

An equivalent metal ion in one- and two-metal-ion catalysis

Wei Yang. Nat Struct Mol Biol. 2008 Nov.

Abstract

Nucleotidyl-transfer enzymes, which synthesize, degrade and rearrange DNA and RNA, often depend on metal ions for catalysis. All DNA and RNA polymerases, MutH-like or RNase H-like nucleases and recombinases, and group I introns seem to require two divalent cations to form a complete active site. The two-metal-ion mechanism has been proposed to orient the substrate, facilitate acid-base catalysis and allow catalytic specificity to exceed substrate binding specificity attributable to the stringent metal-ion (Mg2+ in particular) coordination. Not all nucleotidyl-transfer enzymes use two metal ions for catalysis, however. The betabetaalpha-Me and HUH nucleases depend on a single metal ion in the active site for the catalysis. All of these one- and two metal ion-dependent enzymes generate 5'-phosphate and 3'-OH products. Structural and mechanistic comparisons show that these seemingly unrelated nucleotidyl-transferases share a functionally equivalent metal ion.

PubMed Disclaimer

Figures

Figure 1
Figure 1. A diagram of two-metal ion catalysis by RNase H
Coordination of metal ions A and B is indicated by the dashed lines. The Asp conserved in all nucleotidyl-transfer enzymes using two-metal ions is highlighted in pink. This Asp is replaced by a backbone phosphate in group I introns. The oxygen atoms from the protein and scissile phosphate that chelate metal ion B are highlighted in pink, and the attacking nucleophile is highlighted in blue.
Figure 2
Figure 2. Examples of one-metal ion-dependent nucleases
(A–E) The ββα-Me family. (F) The flipped ββα-Me family. The active site residues are shown in green(C)/blue(N)/red(O) and the DNA substrate centered on the scissile phosphate in yellow(C)/blue/red/orange(P) stick models. The Na+, Mg2+ and Zn2+ in the active site are shown as color-coded spheres. Coordination of metal ion is represented by pink dashed lines. The mobile metal-ion ligand is indicated by a yellow arrow. When determined, the nucleophile water is shown as a red sphere. The adjoining two active site residues in the ββα-Me nucleases are highlighted by the orange ovals. Mutations of the active site residues, which enable crystallization of enzyme-substrate complexes are labeled.
Figure 3
Figure 3. Comparison of the active site of RNase H and TraI in stereoview
The nucleic acid is shown in light grey, and the protein in yellow with the N (blue), O (red), P (meganta) highlighted. The Mg2+ ions are shown as purple spheres, and their coordination by macromolecules is indicated by dashed pink lines. The active site mutations (D192N and Y16F) that prevent the chemistry are labeled. Alignments of the metal ions (or Lys) between the two enzymes are shown by the semi-transparent grey lines. The orange arrows represent the nucleophilic attack.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J. Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Science. 1994;264:1891–903. - PubMed
    1. Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature. 1998;391:251–8. - PubMed
    1. Steitz TA. A mechanism for all polymerases. Nature. 1998;391:231–2. - PubMed
    1. Beese LS, Steitz TA. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. Embo J. 1991;10:25–33. - PMC - PubMed
    1. Lee JY, et al. MutH complexed with Hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage. Mol Cell. 2005;20:155–66. - PubMed

Publication types

MeSH terms