Protein Name

Type I restriction-modification enzyme, specificity subunit


Methanococcus jannaschii (archaea)

Biological Context

DNA restriction enzymes prevent invasion of foreign DNA from phages by cleaving them. There are three types of DNA restriction enzymes, I, II, and III. The type I enzymes recognize two specific double-strand DNA (dsDNA) sequences separated by a given spacer and cleave randomly far from the recognition sequences, which distinguish type I enzymes from other DNA restriction enzymes. The type I enzymes are heterogeneous complexes, composed of a specificity subunit (S-subunit) that recognize a specific DNA sequence, a methylation subunit (M-subunit) that methylates the target adenine nucleotides recognized by S-subunit, and a restriction subunit (R-subunit) that cleaves DNA randomly. The type I enzymes primarily cleaves unmethylated DNA, but they also methylate the target adenine nucleotides in a hemimethylated DNA.

Structure Description


The structure shown here is of the type I specificity subunit (S-subunit) from Methanococcus jannaschii. Two highly conserved regions (CRs) in the middle and at the C terminus form a coiled-coil of long antiparallel alpha-helices, and two target recognition domains (TRDs) forming globular structures are at each end of the coiled-coil structure. The two TRDs have almost identical topologies.

TRD1 (the N-terminal first TRD) and TRD2 (the second TRD) interact with CCR (the central CR) and DCR (the distal CR) respectively, and form DNA binding crefts in both TRDs (see fig.2).

The authors of this paper obtained a model of a DNA complex with the two TRDs using the binding mode of dsDNA and TaqI-MTase, methyltransferase from Thermus aquaticus. When compared with B-DNA, this modeled DNA was kinked at the 8bp spacer between the between the two binding sites. This kink caused unwinding of dsDNA to extrude the target adenine to be modified. The authors suggest that CRs act as a molecular ruler by forming two antiparallel CR helices and providing a proper physical space (8bp) between two binding sites.

Whereas the structure shown here includes two S-subunits, the figure shown in fig.1 is one of the unit.

monomer (Fig.1) The cartoon model of a S-subunit.
CCR:Central Conserved Region
DCR:Distal Conserved Region
TRD1:Target Recognition Domain at N-terminal
TRD2:Target Recognition Domain at C-terminal
DNA_binding_creft (Fig.2) The DNA binding creft of TRD1

Protein Data Bank (PDB)



  • Kim, J.S. Degiovanni, A. Jancarik, J. Adams, P.D. Yokota, H. Kim, R. Kim, S.H.; "Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications."; Proc.Natl.Acad.Sci.USA; (2005) 102:3248-3253 PubMed:15728358.


author: Miho Higurashi

Japanese version:PDB:1YF2