An endodeoxyribonuclease that may play a role in defense against invading genetic elements. Uses short DNA sequences as guides to bind complementary target strands, resulting in slicing of the target DNA (PubMed:24442234, PubMed:27741323, PubMed:28319081, PubMed:28319084). Also has guide-independent activity on target DNA (PubMed:28319081). Probably a first round of guide-independent activity on an invading plasmid or virus would generate guide DNAs for subsequent, more efficient, guide-dependent degradation of invading nucleic acids (PubMed:28319081). Endonucleolytically cleaves DNA in short dsDNA (the guide DNA indicates where to cleave on the target DNA) (PubMed:24442234, PubMed:27741323, PubMed:28319081, PubMed:28319084). Efficient guide-dependent target DNA cleavage requires a minimal length of 15 bp and is maximal at 19 bp (PubMed:28319081). Prefers guide DNA with 5'-phosphorylated purines and 3'-pyrimidines; changing these bases alters the cleavage activity and patterns (PubMed:28319084). Has no activity on substrate with a mismatch at positions 10 and 11, ssDNA or RNA, nor on DNA-RNA hybrids (PubMed:24442234). Digests longer (750 bp) dsDNA as well as circular plasmid and naked genomic DNA, but not chromatin, in a guide DNA-independent manner (PubMed:28319081). Addition of endogenous histone A3 protects DNA from cleavage, while cleavage is insensitive to methylation (PubMed:28319081). When plasmid encoding active or mutated protein (Ala-541) is transformed into Sulfolobus acidocaldarius about 25-fold fewer transformants are found with active protein; reduced levels of plasmid are found in wild-type transformed cells. While S.acidocaldarius grows at a similar temperature to M.jannaschii (70 to 80 degrees Celsius) it has very different histone-like proteins, which presumably do not protect against MjAgo (PubMed:28319081). Binds ssDNA, dsDNA and DNA-RNA hybrids; binding is most efficient with dsDNA (PubMed:24442234). Also liganded by DNA (PubMed:28319084). DNA cleavage is inhibited by EDTA. Optimum temperature is over 75 degrees Celsius for DNA cleavage, DNA-binding occurs below that. Constitutively expressed (at protein level) (PubMed:28319081). Has 4 structurally distinct domains; N-terminal, PAZ (binds the 3'-end of guide DNA), Mid (binds the phosphorylated 5'-end of guide DNA) and PIWI (binds near the 5'-end of guide DNA) arranged in a bilobal manner (PubMed:28319084). Upon binding of guide DNA the PAZ and Mid domains separate, opening a channel probably for target DNA-binding; a smaller channel also opens between the N-terminal and PIWI domains (PubMed:28319084). The N-terminal and PAZ domains undergo further major rearrangement when the binary Ago-guide DNA complex binds target DNA; the PAZ domain binds the 3'-end of guide DNA in the absence of target, upon ternary complex formation it is probably the N-terminal domain that binds that end of the dsDNA (PubMed:24442234). Belongs to the argonaute family. Long pAgo subfamily.