The second ORF of L1 encodes a protein that has endonuclease and reverse transcriptase activity. The encoded protein has a molecular weight of 150 kDa. The structure of the ORF2 protein was solved in 2023. Its protein core contains three domains of unknown functions, termed "tower/EN-linker" and "wrist/RNA-binding domain" that bind Alu RNA's polyA tail and C-terminal domain that binds Alu RNA stem loop.
The nicking and reverse transcriptase activities of L1 ORF2p are boosted by single-stranded DNA structures likely present on the active replication forks. Unlike viral RTs, L1 ORF2p can be primed by RNA, including RNA hairpin primers produced by the Alu element.