Protein Domain : IPR011335

Type:  Domain Name:  Restriction endonuclease type II-like
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. Short Name:  Restrct_endonuc-II-like
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12 Child Features

DB identifier Type Name
IPR011604 Domain Exonuclease, phage-type/RecB, C-terminal
IPR006166 Domain ERCC4 domain
IPR011578 Domain Restriction endonuclease, FokI, C-terminal/endonuclease I, core
IPR011544 Domain Restriction endonuclease, type II, Cfr10/BsoB1, core
IPR011337 Domain DNA mismatch repair MutH/Restriction endonuclease, type II
IPR011338 Domain Restriction endonuclease, type II, BamHI/BglIII/BstY
IPR007560 Domain Restriction endonuclease type IV, Mrr
IPR011336 Domain Restriction endonuclease, type II, EcoRI/MunI
IPR011543 Domain Restriction endonuclease, type II, BglI
IPR007569 Domain Domain of unknown function DUF559
IPR015210 Domain Type-2 restriction enzyme NaeI
IPR015109 Domain Restriction endonuclease, type II, EcoRII, C-terminal

2 Contains

DB identifier Type Name
IPR011856 Domain tRNA endonuclease-like domain
IPR014833 Domain TnsA endonuclease, N-terminal

1 Cross References

Identifier
SSF52980

5 Found Ins

DB identifier Type Name
IPR016889 Family Uncharacterised conserved protein UCP028503
IPR006167 Family DNA repair protein
IPR015278 Family Type-2 restriction enzyme BglII
IPR003509 Family Uncharacterised protein family UPF0102
IPR001616 Family Alphaherpesvirus alkaline exonuclease

0 GO Annotation

0 Ontology Annotations

0 Parent Features

3256 Proteins

DB identifier UniProt Accession Secondary Identifier Organism Name Length
98787 D8RQ83 PAC:15416073 Selaginella moellendorffii 232  
418519 D8S5Z1 PAC:15407325 Selaginella moellendorffii 303  
424147 D8SNZ1 PAC:15422171 Selaginella moellendorffii 343  
447018 D8SW15 PAC:15422176 Selaginella moellendorffii 1259  
76171 D8QSP1 PAC:15413534 Selaginella moellendorffii 266  
403589 D8QRW2 PAC:15408001 Selaginella moellendorffii 359  
90549 D8RCW7 PAC:15413400 Selaginella moellendorffii 933  
evm.TU.contig_28699.1 PAC:16429624 Carica papaya 340  
evm.model.supercontig_197.13 PAC:16412338 Carica papaya 603  
evm.model.supercontig_43.147 PAC:16419959 Carica papaya 323  
evm.model.supercontig_9.243 PAC:16428139 Carica papaya 667  
29929.m004705 B9RMK0 PAC:16813944 Ricinus communis 310  
30128.m008739 B9RF25 PAC:16818328 Ricinus communis 392  
30131.m007247 B9RGF8 PAC:16819068 Ricinus communis 669  
30148.m001484 B9SDH4 PAC:16820628 Ricinus communis 317  
30334.m000029 B9TI34 PAC:16824352 Ricinus communis 163  
35941.m000016 B9TD46 PAC:16826800 Ricinus communis 512  
37457.m000015 B9TDS0 PAC:16827016 Ricinus communis 427  
28266.m000193 B9T527 PAC:16800456 Ricinus communis 666  
27839.m000068 B9TA31 PAC:16799319 Ricinus communis 405  
27940.m000332 B9SZ05 PAC:16799557 Ricinus communis 887  
Cucsa.325730.1 PAC:16977975 Cucumis sativus 390  
Cucsa.325730.2 PAC:16977976 Cucumis sativus 297  
Cucsa.394810.1 PAC:16983256 Cucumis sativus 380  
Cucsa.394810.2 A0A0A0LNG4 PAC:16983257 Cucumis sativus 379  
Cucsa.079500.1 PAC:16956224 Cucumis sativus 288  
Cucsa.137640.1 PAC:16963228 Cucumis sativus 192  
Cucsa.266200.1 A0A0A0LK74 PAC:16973364 Cucumis sativus 671  
Cucsa.308190.1 PAC:16976312 Cucumis sativus 564  
Cucsa.313720.1 PAC:16977045 Cucumis sativus 1002  

4 Publications

First Author Title Year Journal Volume Pages PubMed ID
            15770420
            14576294
            11827971
            11557805