Protein Family Models

This entry represents the topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity [1,2] consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain. The nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. The TOPRIM domain has two conserved motifs, one of which centres at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function [3]. [1]. 32009148. The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases. Schiltz CJ, Adams MC, Chappie JS;. Nucleic Acids Res. 2020;48:2762-2776. [2]. 7836278. The old exonuclease of bacteriophage P2. Myung H, Calendar R;. J Bacteriol. 1995;177:497-501. [3]. 9722641. Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Aravind L, Leipe DD, Koonin EV;. Nucleic Acids Res 1998;26:4205-4213. (from Pfam)

Date:

2024-10-16

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. (from Pfam)

Date:

2024-08-14

This entry contains YjbD from Escherichia coli (Swiss:P75828), which is annotated as a nucleotide triphosphate hydrolase. (from Pfam)

Date:

2024-08-14

OLD (overcoming lysogenization defect)-family ATP-dependent endonuclease may have DNAse as well as RNAse activity; contains a DUF2813 domain

Date:

2018-11-20