How an RNA ligase discriminates RNA versus DNA damage.
T4 RNA ligase 2 (Rnl2) exemplifies a family of RNA-joining enzymes that includes protozoan RNA-editing ligases. Rnl2 efficiently seals 3'-OH/5'-PO4 RNA nicks in either a duplex RNA or an RNA:DNA hybrid but cannot seal DNA nicks. RNA specificity arises from a requirement for at least two ribonucleotides immediately flanking the 3'-OH of the nick; the rest of the nicked duplex can be replaced by DNA. The terminal 2'-OH at the nick is important for the attack of the 3'-OH on the 5'-adenylated strand to form a phosphodiester, but dispensable for nick recognition and adenylylation of the 5'-PO4 strand. The penultimate 2'-OH is important for nick recognition. Stable binding of Rnl2 at a nick depends on contacts to both the N-terminal adenylyltransferase domain and its signature C-terminal domain. Nick sensing also requires adenylylation of Rnl2. These results provide insights to the evolution of nucleic acid repair systems.
Nandakumar
Jayakrishnan
J
Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.
Shuman
Stewart
S
D017122:Bacteriophage T4 / Q000201:enzymology / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004249:DNA Damage; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D011130:RNA Ligase (ATP) / Q000378:metabolism*; D012265:Ribonucleotides / Q000737:chemistry; D013379:Substrate Specificity; D014764:Viral Proteins / Q000378:metabolism*
D012265:Ribonucleotides; D014764:Viral Proteins; D012313:RNA; D004247:DNA; D011130:RNA Ligase (ATP); C467724:bacteriophage T4 RNA ligase 2