UCSC Engineering
(Last Update: 04/18/00 )
Prokaryotic NER involves 3 proteins that carry out the complete process of damage recognition and excision: UvrA, UvrB, and UvrC. UvrA functions as a dimer that complexes with one UvrB to form a UvrA2UvrB complex. This scans DNA in an ATP-dependent manner with helicase properties. When it localizes at a dimer site UvrA dissociates while UvrB is presented to the DNA in a conformation that allows it to bind tightly and specifically. This UvrB-pyrimidine dimer complex acts as a nucleation site for additional enzymes. UvrC binds to the complex and the two proteins then function as a bifunctional nuclease that cuts the damaged strand 4 nucleotides 3' from the dimer followed by a cleavage 7 nucleotides from the 5' side. The catalytic sites for both cleavage reactions reside in the UvrC protein. The 12 nucleotide oligonucleotide is released by the combined action of UvrD (helicase II), DNA polymerase I and DNA ligase. The resulting patch is 12 to 13 nucleotides in length, which corresponds to the footprint of the UvrB:UvrC nuclease on the damaged DNA. This size is characteristic of almost all prokaryotic NER systems. One study has found that an archeal species, M.thermoautotrophicum repairs UV damage by a patch of 10 to 11 nucleotides. The NER system of this organism therefore appears to resemble that of E.coli, although the small difference indicates subtle differences in the conformation or size of the protein components.
UvrB is the central player in this process, which has interaction sites with all of the other proteins involved in NER. UvrB from various prokaryotes contains approximately 650-700 amino acids, and an ATPase site. It is a member of the helicase II superfamily that also contains the eukaryotic repair helicases Rad3 and XPD although the helicase activity may not be the most important activity of UvrB. Binding to DNA damage involves locally denaturated sites, and considerable bending and unwinding of the DNA. Structural studies suggest that it is a functional helicase with the ability to form a tight DNA-UvrB complex by a mechanism involving insertion of a beta hairpin between the two strands of the DNA.
The Uvr genes can be exchanged among different prokaryotes and a UvrB gene from one cell type can be used for complementation of a UvrB mutant E.coli strain either in vivo or in an in vitro assay. Functional analysis can therefore be extended from novel prokaryotes into the more familiar E.coli system with its large set of mutant strains from which to select ones that are appropriate to the question to be solved.
Need to add UVRABC table, and web pages for UVRABC searches.
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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