ligaseAMP

LigaseAMP is a term used in enzymology to describe the transient covalent adenylyl (AMP) intermediate formed during the catalytic cycle of ATP-dependent DNA ligases. These enzymes seal nicks in the DNA backbone by forming a phosphodiester bond, a process essential for DNA replication and various repair pathways. The concept of an ligase-AMP intermediate is a foundational aspect of how ATP-dependent ligases operate at the chemical level.

In the typical catalytic sequence, ATP donates an AMP moiety to a conserved lysine residue on the ligase, generating a ligase-AMP adduct and releasing pyrophosphate. The ligase-AMP then transfers the AMP to the 5'-phosphate of the nicked DNA, creating a DNA-adenylate intermediate. Subsequent attack by the 3'-hydroxyl group completes the phosphodiester bond formation and releases AMP, returning the enzyme to its resting state. This adenylated step is central to the enzyme’s mechanism and is often described in textbooks as the ligase-AMP stage.

DNA ligases exist in ATP-dependent and NAD+-dependent forms across bacteria, archaea, and eukaryotes, with variations in structure and domain organization. ATP-dependent ligases commonly feature catalytic adenylation and DNA-binding domains, enabling efficient nick sealing during replication and repair. In some contexts, the ligand-AMP concept is discussed in relation to RNA ligases and other nucleic-acid–processing enzymes, which can share analogous adenylylation steps.

Terminology wise, LigaseAMP is not a separate enzyme class in standard catalogs; rather, it denotes a mechanistic state—the ligase-AMP intermediate—that is central to the function of ATP-dependent ligases.