Nucleic Acids Research, Vol 26, Issue 18 4205-4213, Copyright © 1998 by Oxford University Press
L Aravind, DD Leipe and EV Koonin
Iterative profile searches and structural modeling show that bacterial
DnaG-type primases, small primase-like proteins from bacteria and archaea,
type IA and type II topoisomerases, bacterial and archaeal nucleases of the
OLD family and bacterial DNA repair proteins of the RecR/M family contain a
common domain, designated Toprim (topoisomerase- primase) domain. The
domain consists of approximately 100 amino acids and has two conserved
motifs, one of which centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). Examination of the structure of Topo IA and
Topo II and modeling of the Toprim domains of the primases reveal a compact
beta/alpha fold, with the conserved negatively charged residues juxtaposed,
and inserts seen in Topo IA and Topo II. The conserved glutamate may act as
a general base in nucleotide polymerization by primases and in strand
rejoining by topoisomerases and as a general acid in strand cleavage by
topoisomerases and nucleases. The role of this glutamate in catalysis is
supported by site-directed mutagenesis data on primases and Topo IA. The
DxD motif may coordinate Mg2+that is required for the activity of all
Toprim-containing enzymes. The common ancestor of all life forms could
encode a prototype Toprim enzyme that might have had both nucleotidyl
transferase and polynucleotide cleaving activity.
ARTICLES
Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins
Department of Biology, Texas A&M University, College Station, TX 70843, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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