Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) TRD1-CR1, Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) TRD1-CR1
The recognition sequences of Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) and Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.
Comment:based on related TRD1-CR1/TRD2-CR2 's with structure
Comment:HsdS DNA specificity subunit, and HsdM DNA modification subunit; type I RM enzymes, are formed from a core methyltransferase (MTase) comprised of one HsdS subunit and two HsdM subunits, this is complexed with two HsdR DNA restriction subunits (R2M2S1)
Comment:CR1 and CR2 refer to two coiled-coiled structures, found at the ends of the primary sequence of S-subunit TRD1 and TRD2 respectively; CR1 and CR2 run antiparallel to each other and interact by hydrophobic contacts between a series of hydrophobic residues
Jiyao W et al.(2023). "The conserved domain database in 2023.",