Atg16L forms an approximately 800 kDa complex with the Atg12-Atg5 conjugate. The Atg16L complex is localized in the isolation membrane (also called the phagophore) under starvation conditions, and facilitates the conjugation of LC3 to PE. Lack of autophagosome formation in Atg16L knockout mice clearly indicates that Atg16L is an essential factor for autophagy.
Atg16L shares high homology with yeast Atg16, but unlike yeast Atg16, carries a large WD repeat domain at the C-terminus. In the WD repeat domain, a sensitive single nucleotide polymorphism (SNP) has been detected for Crohn’s disease, one of the inflammatory bowel diseases of unknown cause. The association of Crohn’s disease with Atg16L is a topic of further study.