The following text describes a protein:
Function:
A catalytically inactive argonaute protein. Binds 5'-phosphorylated RNA as the guide (gRNA) and short DNA as target DNA (tDNA); does not bind other nucleic acid combinations, does not bind tDNA alone. Has highest affinity for gRNA that begins with 5'-phospho-U and poor affinity for gRNA with 5'-OH. Upon expression in E.coli, plasmid sequences are found in RsAgo, its induction leads to plasmid degradation and suppression of genes encoded on foreign plasmids, suggesting it may also interfere with transcription. Does not interact with preformed gRNA:tDNA duplexes. Mismatches and nt bulges are tolerated in the ternary complex, however, they significantly reduce the affinity of RsAgo:gRNA for tDNA. Mismatched tDNA can cause dissociation of gRNA from RsAgo. In situ binds 2 populations of RNA (15-19 and 45 nucleotides, nt) and a population of ssDNA 22-24 nt in length. The small sense RNA is probably derived from mRNA degradation and strongly enriched for U in the first and U/C in the second positions. The small DNA is enriched for sequences complementary to the RNA, with 3 nt overhangs on both ends; another nuclease may trim the ends. The sequences are largely derived from exogenous plasmids or genome-encoded foreign elements such as prophages and transposons. Forms a ternary complex with gRNA and double-stranded tDNA only when the tDNA is open.
Miscellaneous:
MISCELLANEOUS: Argonaute in this bacteria does not have endonuclease activity as the catalytic residues are not conserved, however a nuclease is encoded nearby in the genome (Probable). Restoring the catalytic residues to those conserved in T.thermophilus (G529D, AH604-605RD and E746D) does not reconstitute tDNA cleavage.
Domain:
Has 4 domains (N-terminal, PAZ, Mid and PIWI). The N-terminal and PAZ domains are joined by linker L1, the PAZ and Mid domains are joined by linker L2. The domains assemble in 2 lobes; the PAZ lobe consists of the N-terminal, L1, PAZ and L2 domains, while the PIWI lobe has the Mid and PIWI domains. The PIWI domain assumes an RNase H fold but in this bacteria does not have catalytic activities. The gRNA:tDNA duplex lies between the 2 lobes. The 5'-phosphate and first base of the gRNA bind in the Mid domain, the middle of the gRNA binds to the PAZ domain, while the 3'-region of the gRNA strand base-pairs with the 5'-region of the tDNA strand but not to the PAZ domain. The 5'-region of the tDNA strand binds to RsAgo N-terminal domain in the heteroduplex.
Sequence:
MAPVQAADEMYDSNPHPDRRQLVSNGFEVNLPDQVEVIVRDLPDPSKVKEERTRLMGYWFVHWFDGKLFHLRIKAGGPNVDGEHRAIRTAEHPWLLRARLDDALEEALPKYAAVKKRPFTFLAQKDELIDAAATAAGLSHRLLNSFKVIPRFALSPKIYEPVDGTTRVGVFVTIGMRYDIEASLRDLLEAGIDLRGMYVVRRKRQPGERGLLGRVRAISDDMVQLFEETDLASVNVNDAKLEGSKENFTRCLSALLGHNYKKLLNALDDQEAGYRTGPRFDDAVRRMGEFLAKKPIRLADNINAQVGDRIVFSNEGQARNVRLAPKVEYVFDRTGAKSAEYAWRGLSQFGPFDRPSFANRSPRILVVYPSSTQGKVENFLSAFRDGMGSNYSGFSKGFVDLMGLTKVEFVMCPVEVSSADRNGAHTKYNSAIEDKLAGAGEVHAGIVVLFEDHARLPDDRNPYIHTKSLLLTLGVPTQQVRMPTVLLEPKSLQYTLQNFSIATYAKLNGTPWTVNHDKAINDELVVGMGLAELSGSRTEKRQRFVGITTVFAGDGSYLLGNVSKECEYEGYSDAIRESMTGILRELKKRNNWRPGDTVRVVFHAHRPLKRVDVASIVFECTREIGSDQNIQMAFVTVSHDHPFVLIDRSERGLEAYKGSTARKGVFAPPRGAISRVGRLTRLLAVNSPQLIKRANTPLPTPLLVSLHPDSTFKDVDYLAEQALKFTSLSWRSTLPAATPVTIFYSERIAELLGRLKSIPNWSSANLNIKLKWSRWFL