Adenylation domain of kDNA ligases and similar proteins
The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active-site residues.
Comment:Sealing a nick in DNA requires three catalytic steps: first, enzyme adenylation is accomplished using ATP resulting in an AMP-linkage to the enzyme; second, the AMP is transferred to the 5' phosphate at the site of a nick; and third, phosphoryl transfer and sealing the nicked DNA.
Structure:1FVI_A; Chlorella Virus DNA Ligase binds AMP; contacts at 4A.
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