A novel uracil-DNA glycosylase family related to the helix-hairpin-helix DNA glycosylase superfamily

Abstract

Cytosine bases can be deaminated spontaneously to uracil, causing DNA damage. Uracil-DNA glycosylase (UDG), a ubiquitous uracil-excising enzyme found in bacteria and eukaryotes, is one of the enzymes that repair this kind of DNA damage. To date, no UDG-coding gene has been identified in Methanococcus jannaschii, although its entire genome was deciphered. Here, we have identified and characterized a novel UDG from M.jannaschii designated as MjUDG. It efficiently removed uracil from both single- and double-stranded DNA. MjUDG also catalyzes the excision of 8-oxoguanine from DNA. MjUDG has a helix-hairpin-helix motif and a [4Fe-4S]-binding cluster that is considered to be important for the DNA binding and catalytic activity. Although MjUDG shares these features with other structural families such as endonuclease III and mismatch-specific DNA glycosylase (MIG), unique conserved amino acids and substrate specificity distinguish MjUDG from other families. Also, a homologous member of MjUDG was identified in Aquifex aeolicus. We report that MjUDG belongs to a novel UDG family that has not been described to date.

Arabidopsis Uracil DNA Glycosylase (UNG) Is Required for Base Excision Repair of Uracil and Increases Plant Sensitivity to 5-Fluorouracil

“…The T-DNA is inserted in exon 6 (Fig. 5E), and the mutant AtUNG transcript would presumably encode a truncated protein lacking sequence motif B, which is conserved in all members of the Family-1 of UDGs (6,9). Plants homozygous for the T-DNA insertion were identified by PCR.…”

“…UDGs are distributed across a protein superfamily consisting of five families (6,9). The first UDG identified was the Ung enzyme from Escherichia coli (10), which typifies the ubiquitous Family-1 of UDGs.…”

“…UDGs from families 4 and 5 have been identified in thermophilic bacteria and archaea. In addition to the five UDG families, at least three families of the HhH-GPD superfamily of DNA glycosylases (named after its hallmark helix-hairpin-helix and Gly/Pro-rich loop followed by a conserved aspartate) include members with UDG activity (6,9).…”

The Hyperthermophilic Euryarchaeon Archaeoglobus fulgidus Repairs Uracil by Single-Nucleotide Replacement

“…At present, the information available indicates that family 1 and 2 UDGs are confined to mesophilic organisms (44), whereas family 4 to 6 UDGs and MIG enzymes are present in (hyper)thermophiles (Table 2). For instance, three UDGs belonging to different families have been characterized in the crenarchaeote P. aerophilum (Table 2), while three ORFs belonging to UDG families 4, 5, and 6 have been identified in Sulfolobus solfataricus (7,49,69), and one of the corresponding proteins has been characterized (11).…”

Trypanosoma cruzi Contains a Single Detectable Uracil-DNA Glycosylase and Repairs Uracil Exclusively Via Short Patch Base Excision Repair

“…6 Uracil DNA glycosylases form a protein superfamily consisting of five families. 12,13 Family-1 enzymes (comprising human UNG and Escherichia coli Ung) are active against uracil in ssDNA and dsDNA, and recognise uracil in an extrahelical conformation. Family-2 enzymes (comprising human TDG and E. coli Mug) are mismatch specific and recognise the widowed guanine in the complementary strand.…”