InterPro : IPR007409

Name  Restriction endonuclease, type I, HsdR, N-terminal Short Name  Restrct_endonuc_type1_HsdR_N
Type  Domain Description  There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below:Type I enzymes () cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase () activities.Type II enzymes () cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.Type III enzymes () cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase ().Type IV enzymes target methylated DNA.Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (), methylase () and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID.Type III restriction endonucleases () are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ].This entry represents the N-terminal domain found in both the R subunit (HsdR) of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoRI, which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity [, , ].This domain is often found adjacent to a methylase domain () in restriction endonucleases or methylases. In one of the proteins, , it is adjacent to a helicase domain () in a putative restriction endonuclease.

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



0 Child Features

0 Contains

2 Found In

Id Name Short Name Type
IPR004473 Restriction endonuclease, type I, HsdR Restrct_endonuc_typeI_HsdR Family
IPR017035 Uncharacterised conserved protein UCP035009, HsdR, All3000-type UCP035009_HsdR_All3000-type Family

0 Parent Features

6 Publications

First Author Title Year Journal Volume Pages
Sistla S S-Adenosyl-L-methionine-dependent restriction enzymes. 2004 Crit Rev Biochem Mol Biol 39 1-19
Bourniquel AA Complex restriction enzymes: NTP-driven molecular motors. 2002 Biochimie 84 1047-59
Williams RJ Restriction endonucleases: classification, properties, and applications. 2003 Mol Biotechnol 23 225-43
Piekarowicz A Analysis of type I restriction modification systems in the Neisseriaceae: genetic organization and properties of the gene products. 2001 Mol Microbiol 41 1199-210
Makovets S Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes. 1999 Proc Natl Acad Sci U S A 96 9757-62
Murray NE Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes. 1993 Mol Microbiol 9 133-43

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)