REBASE--restriction enzymes and DNA methyltransferases

Abstract

REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in restriction-modification. It contains both published and unpublished work with information about recognition and cleavage sites, isoschizomers, commercial availability, crystal and sequence data. Experimentally characterized homing endonucleases are also included. Additionally, REBASE contains complete and up-to-date information about the methylation sensitivity of restriction endonucleases. An extensive analysis is included of the restriction-modification systems that are predicted to be present in the sequenced bacterial and archaeal genomes from GenBank. The contents of REBASE are available by browsing from the web (http://rebase.neb.com/rebase/rebase.html) and through selected compilations by ftp (ftp.neb.com) and as monthly updates that can be requested via email.

Figure 1

The circles depict the four major types of restriction enzymes and show the occurrence of their components in REBASE. The Type I enzymes have three genes encoding a methyltransferase subunit, a restriction subunit and a specificity subunit. The Type II enzymes have two separate genes, one encoding a restriction enzyme and one encoding a methyltransferase. The Type III enzymes also have two genes, one encoding a methyltransferase, which can operate alone or form part of a complex with a restriction subunit. The Type IV enzymes act alone and restrict DNA that is methylated. The solid colors indicate REBASE entries that have been experimentally verified and the shaded colors indicate genes predicted computationally. R genes are in red, M genes in blue and specificity genes in yellow. The numbers refer to the contents of REBASE on September 15, 2004.