WHAT IS REBASE ?
The Restriction Enzyme Database – Restriction Enzyme data BASE
A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding.
The Restriction Enzyme Database
The four basic types of restriction systems (I-IV)
The key characteristics of the Type I R-M systems are that these enzymes are multisubunit proteins that function as a single protein complex and usually contain two R subunits, two M subunits, and one S subunit. After locating their recognition site they serve as molecular motors to translocate DNA until a collision occurs that triggers cleavage. The resulting fragments thus tend to be fairly random.
The Type II restriction systems typically contain individual restriction enzymes and modification enzymes encoded by separate genes. The Type II restriction enzymes typically recognize specific DNA sequences and cleave at constant positions at or close to that sequence to produce 5-phosphates and 3-hydroxyls. Usually they require Mg2+ ions as a cofactor, although some have more exotic requirements. The methyltransferases usually recognize the same sequence although some are more promiscuous. Three types of DNA methyltransferases have been found as part of Type II R-M systems forming either C5-methylcytosine, N4-methylcytosine or N6-methyladenine.
These systems are composed of two genes (mod and res) encoding protein subunits that function either in DNA recognition and modification (Mod) or restriction (Res). Both subunits are required for restriction, which also has an absolute requirement for ATP hydrolysis. For DNA cleavage, the enzyme must interact with two copies of a non-palindromic recognition sequence and the sites must be in an inverse orientation in the substrate DNA molecule. Cleavage is preceded by ATP-dependent DNA translocation as with the Type I REases. The enzymes cleave at a specific distance away from one of the two copies of their recognition sequence. The Mod subunit can function independently of the Res subunit to methylate DNA: in all known cases the methylated base formed is N6-methyladenine and full modification is actually hemi-methylation.
These systems are composed of one or two genes encoding proteins that cleave only modified DNA, including methylated, hydroxymethylated and glucosyl-hydroxymethylated bases. Their recognition sequences have usually not been well defined except for EcoKMcrBC, which recognizes two dinucleotides of the general form RmC (a purine followed by a methylated cytosine either m4C or m5C) and which are separated by anywhere from 40-3000 bases. Cleavage takes place approximately 30 bp away from one of the sites.
The standard nomenclature for restriction enzymes, DNA methyltransferases and related proteins can be found in Roberts et al. 2005 Nucl. Acids Res. 31: 1805-1812 (REBASE ref 7998).
RECOGNITION SEQUENCE NOMENCLATURE
REBASE Recognition sequences representations use the standard abbreviations
(Eur. J. Biochem. 150: 1-5, 1985) to represent ambiguity:
R = G or A
Y = C or T
M = A or C
K = G or T
S = G or C
W = A or T
B = not A (C or G or T)
D = not C (A or G or T)
H = not G (A or C or T)
V = not T (A or C or G)
N = A or C or G or T
These are written from 5′ to 3′, when only one strand is shown.
Typically, the recognition sequences are oriented so that the cleavage sites lie on their 3′ side.
Homing endonucleases do not really have recognition sequences in the way that restriction enzymes do. The recognition sequence listed is one site that is known to be recognized and cleaved. In general, single base changes merely change the efficiency of cleavage and the precise boundary of required bases is not known.
For putative enzymes, the recognition sequences are predicted.