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ADDB, N-terminal
ATP-dependent helicase/deoxyribonuclease subunit B (ADDB) forms a heterodimer with ADDA which acts as both an ATP-dependent DNA helicase and an ATP-dependent single-stranded exonuclease, acting in both directions. This entry represents the N-terminal domain of ADDB, which contains the Walker A motif involved in ATP binding [1,2]. Paper describing PDB structure 3u44. [1]. 22307084. Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex. Saikrishnan K, Yeeles JT, Gilhooly NS, Krajewski WW, Dillingham MS, Wigley DB;. EMBO J. 2012;31:1568-1578. Paper describing PDB structure 4ceh. [2]. 24670664. Structural basis for translocation by AddAB helicase-nuclease and its arrest at chi sites. Krajewski WW, Fu X, Wilkinson M, Cronin NB, Dillingham MS, Wigley DB;. Nature. 2014;508:416-419. (from Pfam)
3'-5' exonuclease
This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold. (from Pfam)
PD-(D/E)XK nuclease family protein
Members of this family belong to the PD-(D/E)XK nuclease superfamily [1]. 15972856. Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Kinch LN, Ginalski K, Rychlewski L, Grishin NV;. Nucleic Acids Res. 2005;33:3598-3605. (from Pfam)
helicase-exonuclease AddAB subunit AddB
DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. Nevertheless, the partner is designated AddB in both systems. This model describes the AddB protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous, functionally equivalent, and merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function.
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