The following text describes a protein:
Function:
A DNA-guided ssDNA endonuclease that may play a role in defense against invading genetic elements. Uses short ssDNA sequences as guides (gDNA) to bind complementary target strands, resulting in slicing of the target DNA (tDNA). Endonucleolytically cleaves tDNA (the gDNA indicates where to cleave); two major and two minor products are seen which correspond to cleavage sites between nucleotides 9/10, 10/11, 13/14, and 14/15 downstream of the target residue base-paired with the 5'-end of the gDNA. Efficient guide-dependent tDNA cleavage requires a minimal length of 15 bp and is maximal at 19 bp. Prefers gDNA with 5'-phosphorylated purines and 3'-pyrimidines; changing these bases alters the cleavage activity and patterns. Also has guide-independent activity on tDNA called 'chopping'. 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. Has no activity on substrate with a mismatch at positions 10 and 11, on ssDNA or RNA, nor on DNA:RNA hybrids. Digests longer (750 bp) dsDNA as well as circular plasmid and naked genomic DNA, but not chromatin, in a guide DNA-independent manner. Addition of endogenous histone A3 protects DNA from cleavage, while cleavage is insensitive to methylation. 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. Binds ssDNA, dsDNA and DNA-RNA hybrids; binding is most efficient with dsDNA.
Domain:
Has 4 structurally distinct domains; N-terminal, PAZ (binds the 3'-end of gDNA), Mid (binds the phosphorylated 5'-end of gDNA) and PIWI (binds near the 5'-end of gDNA) arranged in a bilobal manner. Upon binding of gDNA the PAZ and Mid domains separate, opening a channel probably for tDNA-binding; a smaller channel also opens between the N-terminal and PIWI domains. The N-terminal and PAZ domains undergo further major rearrangement when the binary Ago-guide DNA complex binds tDNA; the PAZ domain binds the 3'-end of gDNA in the absence of target, upon ternary complex formation it is probably the N-terminal domain that binds that end of the dsDNA. The PIWI domain assumes an RNase H fold and has the catalytic residues.
Sequence:
MVLNKVTYKINAYKIKEEFIPKEVHFYRIKSFVNEAFNFYRFVNFYGGMIINKKDKSFVLPYKVDNKVLKYKDGNNEIPIDIEYIKSLKLEYVKPEIAEKLVRGYLKSVHKIEPELSRIIKNIRKHKVVENIKVESYCEYEVKKHDGDYYLILNFRHTASITKHLWDFVNRDKALLEEYVGKKIIFKPNPKVRYTISLVDAPNPQKIEEIMSHIIKYYKWSEDMVKSTFGEIDYNQPIMYCEEILEPFAPQFCNLVFYMDELDSYILKELQSYWRLSNENKGKIINEIAKKLRFIDNTPKELEFMKFNNTPLLVKDVNKNPTKIYSTNTLFTWIYNQNAKIYLPYDVPEIIRNKNLLTYILIDEEIKDELKAIKDKVNKMFRNYNKIANKTELPKFNYANRWKYFSTDDIRGIIKEIKSEFNDEICFALIIGKEKYKDNDYYEILKKQLFDLKIISQNILWENWRKDDKGYMTNNLLIQIMGKLGIKYFILDSKTPYDYIMGLDTGLGIFGNHRVGGCTVVYDSEGKIRRIQPIETPAPGERLHLPYVIEYLENKANIDMENKNILFLRDGFIQNSERNDLKEISKELNSNIEVISIRKNNKYKVFTSDYRIGSVFGNDGIFLPHKTPFGSNPVKLSTWLRFNCGNEEGLKINESIMQLLYDLTKMNYSALYGEGRYLRIPAPIHYADKFVKALGKNWKIDEELLKHGFLYFI