5G5T | pdb_00005g5t

Structure of the Argonaute protein from Methanocaldcoccus janaschii in complex with guide DNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribonuclease H-like	8053656	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PAZ domain	8053654	3001750	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mid domain of argonaute	8053655	3002210	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)
A	COG1431_3rd	e5g5tA4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: COG1431_3rd	ECOD (1.6)
A	COG1431_2nd_1	e5g5tA5	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: COG1431_2nd_1	ECOD (1.6)
A	COG1431_1st	e5g5tA3	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: COG1431_1st	ECOD (1.6)
A	COG1431_4th	e5g5tA1	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: COG1431_4th	ECOD (1.6)
A	Piwi_C_1	e5g5tA2	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)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (utative)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22333	Argonaute, PAZ domain, archaea (Ago_PAZ_arc)	Argonaute, PAZ domain, archaea	This entry represents the PAZ domain of archaeal argonaute (Ago) [1]. Ago is a DNA-guided ssDNA endonuclease that may play a role in defense against invading genetic elements that uses short ssDNA sequences as guides (gDNA) to bind complementary targ ...	This entry represents the PAZ domain of archaeal argonaute (Ago) [1]. Ago is a DNA-guided ssDNA endonuclease that may play a role in defense against invading genetic elements that uses short ssDNA sequences as guides (gDNA) to bind complementary target strands resulting in slicing of the target DNA (tDNA) [1,2].	Domain
A	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
A	PF22138	Archaeal argonaute protein N-terminal domain (MjAgo_N-like)	Archaeal argonaute protein N-terminal domain	Argonaute (Ago) proteins are found in all three domains of life. They share a common molecular architecture, with the C-terminal lobe consisting of the middle (Mid) and PIWI (P element wimpy testis) domains and the N-terminal lobe containing the N-te ...	Argonaute (Ago) proteins are found in all three domains of life. They share a common molecular architecture, with the C-terminal lobe consisting of the middle (Mid) and PIWI (P element wimpy testis) domains and the N-terminal lobe containing the N-terminal and PIWI-Argonaute-Zwille (PAZ) domains. Archaeal argonaute proteins are guided by 5'-phosphorylated DNA strands and exclusively process cognate DNA targets. This entry represents the N-terminal domain of the archaeal argonaute protein found in M.jannaschii. This domain consists of a four stranded antiparallel beta-sheet and an alpha-helix [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D]	GUIDE DNA	-	-	-
A	ARGONAUTE	DNA binding binding nucleic acid binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity RNA binding cation binding ion binding metal ion binding DNA binding binding nucleic acid binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity RNA binding cation binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus defense response to symbiont clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids defense response to other organism	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR054390	Argonaute, N-terminal domain, archaea	Domain
A	IPR003100	PAZ domain	Domain
A	IPR036085	PAZ domain superfamily	Homologous Superfamily
A	IPR054436	Argonaute, PAZ domain, methanocaldococcus	Domain
A	IPR003165	Piwi domain	Domain
A	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.