InterPro : IPR011335

Name  Restriction endonuclease type II-like Short Name  Restrct_endonuc-II-like
Type  Domain Description  Type II restriction endonucleases () are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the core structure found in most type II restriction endonucleases, consisting of a 3-layer alpha/beta/alpha topology with mixed beta-sheets. This core structure can be found in the restriction endonucleases EcoRI, EcoRV, BamHI, BglI, BglII, BstyI, PvuII, MunI, NseI, NgoIV, BsobI, HincII, MspI, FokI (C-terminal), EcoO109IR, as well as in lamba exonuclease, DNA mismatch repair protein MutH, VSR (very short repair) endonucleases, TnsA endonucleases (N-terminal), endonucleases I (Holliday junction resolvase), Hjc-like enzymes, XPF/Rad1/Mus81 nucleases, RecB and RecC exodeoxyribonuclease V (C-terminal), and RecU-like enzymes.

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



12 Child Features

Id Name Short Name Type
IPR006166 ERCC4 domain ERCC4_domain Domain
IPR011604 Exonuclease, phage-type/RecB, C-terminal Exonuc_phg/RecB_C Domain
IPR011337 DNA mismatch repair MutH/Restriction endonuclease, type II DNA_rep_MutH/RE_typeII Domain
IPR011338 Restriction endonuclease, type II, BamHI/BglIII/BstY BamHI/BglII/BstY Domain
IPR007560 Restriction endonuclease type IV, Mrr Restrct_endonuc_IV_Mrr Domain
IPR007569 Domain of unknown function DUF559 DUF559 Domain
IPR015210 Type II restriction endonuclease, NaeI Restrct_endonuc_NaeI Domain
IPR015109 Restriction endonuclease, type II, EcoRII, C-terminal Restrct_endonuc_II_EcoRII_C Domain
IPR011578 Restriction endonuclease, FokI, C-terminal/endonuclease I, core Restrct_endonuc_C/endonuc_I Domain
IPR011543 Restriction endonuclease, type II, BglI Restrct_endonuc_II_BglI Domain
IPR011544 Restriction endonuclease, type II, Cfr10/BsoB1, core Restrct_endonuc_II_Cfr10/BsoB1 Domain
IPR011336 Restriction endonuclease, type II, EcoRI/MunI Restrct_endonuc_II_EcoRI/MunI Domain

2 Contains

Id Name Short Name Type
IPR011856 tRNA endonuclease-like domain tRNA_endonuc-like_dom Domain
IPR014833 TnsA endonuclease, N-terminal TnsA_N Domain

5 Found In

Id Name Short Name Type
IPR003509 Uncharacterised protein family UPF0102 UPF0102 Family
IPR001616 Alphaherpesvirus alkaline exonuclease Herpes_alk_exo Family
IPR016889 Uncharacterised conserved protein UCP028503 UCP028503 Family
IPR006167 DNA repair protein Rad1 Family
IPR015278 Restriction endonuclease, type II, BglII Restrct_endonuc_II_BglII Family

0 Parent Features

4 Publications

First Author Title Year Journal Volume Pages
Pingoud A Type II restriction endonucleases: structure and mechanism. 2005 Cell Mol Life Sci 62 685-707
Mucke M Diversity of type II restriction endonucleases that require two DNA recognition sites. 2003 Nucleic Acids Res 31 6079-84
Pingoud V Evolutionary relationship between different subgroups of restriction endonucleases. 2002 J Biol Chem 277 14306-14
Pingoud A Structure and function of type II restriction endonucleases. 2001 Nucleic Acids Res 29 3705-27

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)