Catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6 [goid 16874] [evidence IEA]; Catalysis of ATP-dependent isopeptide bond formation between the carboxy-terminal residues of a small conjugating protein such as ubiquitin or a ubiquitin-like protein, and a substrate lysine residue. This function may be performed alone or in conjunction with an E3, ubiquitin-like protein ligase [goid 19787] [evidence IEA]; Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) [goid 5515] [pmid 14516784] [evidence IPI]; Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) [goid 5515] [pmid 12072434] [evidence IPI]; Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) [goid 5515] [pmid 9885291] [evidence IPI]; Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) [goid 5515] [pmid 12072434] [evidence IPI]; Catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6 [goid 16874] [evidence IEA]; Catalysis of ATP-dependent isopeptide bond formation between the carboxy-terminal residues of a small conjugating protein such as ubiquitin or a ubiquitin-like protein, and a substrate lysine residue. This function may be performed alone or in conjunction with an E3, ubiquitin-like protein ligase [goid 19787] [evidence IEA]; Interacting selectively with Helix Loop Helix, a domain of 40-50 residues that occurs in specific DNA-binding proteins that act as transcription factors. The domain is formed of two amphipathic helices joined by a variable length linker region that can form a loop and it mediates protein dimerization [goid 43398] [evidence IEA]