UCSC Engineering
Base-repair proteins are those that recognize specific damage to DNA and repair it directly (as opposed to base-excision which removes bad bases and lets other enzymes fix up the resulting holes).
The DNA photolyases are perhaps the best studied family. They use a pair of chomophores to capture a photon and use it to transfer an electron to break up pyrimidine dimers. They occur in bacteria, archea, and eukaryotes, but are not ubiquitous (for example, S. cerevisiae has a DNA photolyase, but S. pombe does not).
At least three classes are known: one uses FADH and folate (E. coli, S. cerevisiae), one uses FADH and deazaflavin (M. thermoautotrophicum, ...) and one has been found in a metazoan (Carassius auratus). A similar plant protein (HY4) has been identified---does it have DNA photorepair activity?
General discussion of similarity between the different classes needed here.
Table needed here with pointers to pages for individual sequences.
There is probably a 6-4 photorepair action in Drosophila melanogaster. Has the enzyme been identified yet?
Information needed here for the spore photoproduct in B. subtilis and its repair enzyme (gene spl+).
Is this the right page for alkylation repair (such as by enzymes O6 MGT I (ada+ gene) and O6 MGT II (ogt+ gene) in E. coli)? Or should they have their own page. Note that the MGT enzymes seem to have a common domain, which includes a C X3 C X26 C X2 C zinc finger.
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The Bioinformatics group at UCSC is supported in part by NSF grant BIR-9408579, NSF grant MIP-9488395, DOE grant DE-FG03-95ER62112, LACOR grant 4158U0015-3A-01, and by GANN and NSF graduate fellowships.
The DNA-repair pages are not currently funded, so development of them is very slow.
Questions about page content should be directed to
Kevin Karplus