Protein: Protein argonaute (Q746M7)
Organism: Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Function: A DNA-guided ssDNA endonuclease. Uses short ssDNA sequences as guides (gDNA, also called small interfering DNA, siDNA) to bind complementary DNA target strands, resulting in cleavage of the target DNA (tDNA). The cleavage site is 10 nucleotides (nt) downstream of the target residue base-paired with the 5'-end of the gDNA. Plays a role in completion of DNA replication, participates in decatenating replicated DNA and plasmid. In situ purifies with 5'-phosphorylated long DNA (about 1160 nt, maps to the whole chromosome and plasmid), 25-35 nt RNAs that map to the whole chromosome and 15-18 nt DNA that maps to the replication terminus region (ter) on the chromosome and plasmid. Most short DNA starts with dC. Has been shown to have guide sequence-independent dsDNase activity called 'chopping', which requires unstable DNA (high AT-content, multiple mismatches or low salt conditions), and could be used to generate gDNA. Preferentially binds tDNA with dC at its 3'- terminus. Has also been shown to have no detectable guide sequence-independent dsDNase activity. The latter study proposes TtAgo may acquire gDNA from nicked dsDNA, by binding to 5'-phosphorylated-dC nicks, then cleaving 10 nt away on the opposite strand; subsequently an exonuclease (maybe AddA-AddB helicase/nuclease) trims the ends to generate the gDNA (Probable)
Sequence: MNHLGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLEDLHEEEGSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV
InterPro domains: - IPR040895: Argonaute, PAZ domain (domain) [181-263]
- IPR012337: Ribonuclease H-like superfamily (homologous_superfamily) [282-685]
- IPR003165: Piwi domain (domain) [404-671]
- IPR054764: Argonaute, N-terminal domain, thermus (domain) [26-96]
- IPR054763: Argonaute, middle domain (domain) [327-444]
- IPR003100: PAZ domain (domain) [169-265]
- IPR036397: Ribonuclease H superfamily (homologous_superfamily) [467-685]
Gene Ontology annotations:
Molecular Function (MF): GO:0003674 (molecular function), GO:0005488 (binding), GO:0005515 (protein binding)
Biological Process (BP): GO:0008150 (biological process), GO:0008152 (metabolic process), GO:0009987 (cellular process), GO:0016032 (viral process), GO:0009058 (biosynthetic process), GO:0044237 (cellular metabolic process), GO:0019058 (viral life cycle), GO:0071704 (organic substance metabolic process), GO:0044238 (primary metabolic process), GO:0006807 (nitrogen compound metabolic process), GO:0019079 (viral genome replication), GO:0044249 (cellular biosynthetic process), GO:0006725 (cellular aromatic compound metabolic process), GO:1901360 (organic cyclic compound metabolic process), GO:0034641 (cellular nitrogen compound metabolic process), GO:1901576 (organic substance biosynthetic process), GO:0006139 (nucleobase-containing compound metabolic process), GO:0043170 (macromolecule metabolic process), GO:0046483 (heterocycle metabolic process), GO:0009059 (macromolecule biosynthetic process), GO:1901362 (organic cyclic compound biosynthetic process), GO:0044271 (cellular nitrogen compound biosynthetic process), GO:0090304 (nucleic acid metabolic process), GO:0034654 (nucleobase-containing compound biosynthetic process), GO:0019438 (aromatic compound biosynthetic process), GO:0018130 (heterocycle biosynthetic process), GO:0016070 (RNA metabolic process), GO:0032774 (RNA biosynthetic process), GO:0097659 (nucleic acid-templated transcription), GO:0006351 (DNA-templated transcription), GO:0006366 (transcription by RNA polymerase II)
Cellular Component (CC): GO:0005575 (cellular component), GO:0110165 (cellular anatomical entity), GO:0005622 (intracellular anatomical structure), GO:0043226 (organelle), GO:0005737 (cytoplasm), GO:0031974 (membrane-enclosed lumen), GO:0043233 (organelle lumen), GO:0043229 (intracellular organelle), GO:0043227 (membrane-bounded organelle), GO:0043228 (non-membrane-bounded organelle), GO:0043231 (intracellular membrane-bounded organelle), GO:0070013 (intracellular organelle lumen), GO:0043232 (intracellular non-membrane-bounded organelle), GO:0031981 (nuclear lumen), GO:0005730 (nucleolus), GO:0005634 (nucleus)