Table 1.
Classification of REase structures
| REase | PDB code boundaries | Order of secondary-structure elements | Class notation | Class | CATH topology | FSSP/DALI fold | α/β | Recognition sequence | Blunt/sticky | Subtype |
|---|---|---|---|---|---|---|---|---|---|---|
| MunI | 1d02B | H1S1S2S3H4S4H3S5(↑)H2 | H1-S-H2-up | I | 3.40.580 | 263 | α | C⁁AATTG | 5′ end | IIP |
| K3-D202 | (ECORI) | |||||||||
| Cfr10I | 1cfr | H1S1S2S3H4S4H3S5(↑)H2 | H1-S-H2-up | I | 3.40.91 | 263 | α | R⁁CCGGY | 5′ end | IIF |
| M1-L283 | (Restr. Endonuc) | |||||||||
| Bse634I | 1knvA | H1S1S2S3H4S4H3S5(↑)H2 | H1-S-H2-up | I | 3.40.91 | 263 | α | R⁁CCGGY | 5′ end | IIF |
| N4-K293 | (Restr. Endonuc) | |||||||||
| EcoRII | 1na6B | H1S1S2S3H4S4H3S5(↑)H2 | H1-S-H2-up | I | not in CATH | 404 | α | ⁁CCWGG | 5′ end | IIE |
| Y183-D402 | ||||||||||
| EcoO109I | 1wtdB | H1S1S2S3H4S4H3S5(↑)S6(↑)H2 | H1-S-H2-up | I | not in CATH | 2501 | α | RG⁁GNCCY | 5′ end | IIP |
| M1-E272 | ||||||||||
| BsoBI | 1dc1A | H1S-2(↑)S-3(↓)S-1(↓)S1S2S3H4S4H3S5(↑)H2 | H1-S-H2-up | I | 3.40.91 | 263 | α | C⁁YCGRG | 5′ end | IIP |
| K5-I323 | (Restr. Endonuc) | |||||||||
| FokI | 2fokA | H1S1S2S3H4S4H3S5(↑)H2S6(↑) | H1-S-H2-up | I | 3.40.91 | 263 | α | GGATGNNNNNNNNN⁁NNNN | 5′ end | IIS |
| P405-F579 | (Restr. Endonuc) | |||||||||
| NgoMIV | 1fiuA | H1S1S2S3H4S4H3S5(↑)S6(↑)H2 | H1-S-H2-up | I | 3.40.50 | 263 | α | G⁁CCGGC | 5′ end | IIF |
| M1-V286 | (Rossmann fold) | |||||||||
| EcoRI | 1qc9A | H1S1S2S3H4S4H3S5(↑)H2 | H1-S-H2-up | I | 3.40.580 | 263 | α | G⁁AATTC | 5′ end | IIP |
| S17-K277 | (ECORI) | |||||||||
| Ecl18kI | 2fqzA | H1S1S2S3H4S4H3S5(↑)S6(↑) H2 | H1-S-H2-up | I | not in CATH | not in FSSP | α | ⁁CCNGG | 5′ end | IIP |
| L4-A302 | ||||||||||
| BstYI | 1sdoA | S6(↓)H2H1S1S2S3H4S4H3S5(↑) | H2-H1-S-up | II | not in CATH | 264 | α | R⁁GATCY | 5′ end | IIP |
| M1-P203 | ||||||||||
| BamHI | 2bamA | S6(↓)H2H1S1S2S3H4S4H3S5(↑) | H2-H1-S-up | II | 3.40.91 | 264 | α | G⁁GATCC | 5′ end | IIP |
| M1-K207 | (Restr. Endonuc) | |||||||||
| BglII | 1dfmA | S6(↓)H2H1S1S2S3H4S4H3S5(↑) | H2-H1-S-up | II | 3.40.91 | 264 | α | A⁁GATCT | 5′ end | IIP |
| M1-M30;D49-E172 | (Restr. Endonuc) | |||||||||
| MspI | 1sa3A | H1H2S1S2S3H4S4S5(↓)H3 | H1-H2-S-down | III | not in CATH | 275 | β | C⁁CGG | 5′ end | IIP |
| M1-G262 | ||||||||||
| HinP1I | 1ynmA | S6(↑)H1H2S1S2S3H4S4S5(↓)H3 | H1-H2-S-down | III | not in CATH | not in FSSP | β | G⁁CGC | 5′ end | IIP |
| G7-I247 | ||||||||||
| HincII | 1xhvA | H2S6(↑)H1S1S2S3H4S4S5(↓) | H2-H1-S-down | IV | 3.40.600 | not in FSSP | β | GTY⁁RAC | blunt | IIP |
| S2-L258 | (ECORV) | |||||||||
| EcoRV | 1b94A | H2H1S1S2S3S4S5(↓)H3 | H2-H1-S-down | IV | 3.40.600 | 270 | β | GAT⁁ATC | blunt | IIP |
| S2-K245 | (ECORV) | |||||||||
| NaeI | 1iawA | H2H1S1S2S3S4S5(↓)H3S6(↑) | H2-H1-S-down | IV | 3.40.600 | 268 | β | GCC⁁GGC | blunt | IIE |
| E10-E171 | (ECORV) | |||||||||
| BgII | 1dmuA | H2H1S1S2S3S4S5(↓)S6(↑) | H2-H1-S-down | IV | 3.40.600 | 268 | β | GCCNNNN⁁NGGC | 3′ end | IIP |
| M1-K299 | (ECORV) | |||||||||
| SfiI | 2ezvA | H2H1S1S2S3S4S5(↓)H3S6(↑) | H2-H1-S-down | IV | not in CATH | not in FSSP | β | GGCCNNNN⁁NGGCC | 3′ end | IIF |
| M1-R269 | ||||||||||
| PvuII | 3pviA | H1S1S2S3H4S4S5(↓)H3S6(↑) | H1-S-down | V | 3.40.210 | 268 | β | CAG⁁CTG | blunt | IIP |
| S2-Y157 | (PvuII) | |||||||||
| SdaI | 2ixsA | H1S1S-1(↓)S2S3H4S4H3S5(↑)S6(↓) | H1-S-up | VI | not in CATH | not in FSSP | α | CCTGCA⁁GG | 3′ end | IIP |
| P175-R323 |
The columns are ordered as follows: REase column lists the names of the REases; PDB code column lists the pdb files and the residues used in the analysis; Order of secondary structure elements is given in terms of elements that are defined in the ‘material send methods’ section, (↑) and (↓) designate S5 parallel and antiparallel to S1, respectively. Class notation describes the sequential order of the elements and the direction of the S5 strand with respect to the S1 strand. For example, H1-S-H2-up means that H1 is followed by five β-strands (S), followed by helix H2. S5 is parallel to S1 (up); Class indicates the Class number. These are followed (up); Class indicates the Class number. These are followed by CATH topology classification (18), 3.40 is three-layer αβα sandwich; DALI/FSSP fold classification (32); α/β notation, where α-class stands for S5 strand parallel to S1 strand and β-class stands for S5 antiparallel to S1 (11,21,23–25); Recognition sequences (and cleavage sites, designated by ⁁), obtained from REBASE http://rebase.neb.com/rebase/rebase.html; Blunt/sticky classification, where ‘sticky’ leave 5′ or 3′ DNA end overhang and blunt leave no overhangs upon cleavage; Subtype lists the functional subtypes as defined in the REase nomenclature (1).