1YTU | pdb_00001ytu

Structural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth B]	d1ytub2	Alpha and beta proteins (a/b)	Phosphotyrosine protein phosphatases I-like	PIWI domain N-terminal-like	PIWI domain N-terminal	Hypothetical protein AF1318	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
F [auth B]	d1ytub3	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	PIWI domain C-terminal	Hypothetical protein AF1318	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
E [auth A]	d1ytua2	Alpha and beta proteins (a/b)	Phosphotyrosine protein phosphatases I-like	PIWI domain N-terminal-like	PIWI domain N-terminal	Hypothetical protein AF1318	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
E [auth A]	d1ytua3	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	PIWI domain C-terminal	Hypothetical protein AF1318	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8033004	3000143	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Mid domain of argonaute	8053603	3002210	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Mid domain of argonaute	8053603	3002210	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8033004	3000143	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth B]	Piwi_N_2	e1ytuB3	A: a/b three-layered sandwiches	X: Middle domain in Argonaute homologs (From Topology)	H: Middle domain in Argonaute homologs (From Topology)	T: Middle domain in Argonaute homologs	F: Piwi_N_2	ECOD (1.6)
F [auth B]	Piwi_C_1	e1ytuB2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Piwi_C_1	ECOD (1.6)
E [auth A]	Piwi_N_2	e1ytuA4	A: a/b three-layered sandwiches	X: Middle domain in Argonaute homologs (From Topology)	H: Middle domain in Argonaute homologs (From Topology)	T: Middle domain in Argonaute homologs	F: Piwi_N_2	ECOD (1.6)
E [auth A]	Piwi_C_1	e1ytuA3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Piwi_C_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth B]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F [auth B]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
E [auth A]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E [auth A]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B]	PF02171	Piwi domain (Piwi)	Piwi domain	This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as S ...	This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex [2]. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth B]	hypothetical protein AF1318	DNA binding binding nucleic acid binding RNA binding cation binding ion binding metal ion binding small molecule binding	-	-
B [auth D], D [auth F]	5'-R(PUPGPUPC)-3'	-	-	-
A [auth C], C [auth E]	5'-R(PAPGPAPCPAPG)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR003165	Piwi domain	Domain
E [auth A], F [auth B]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.