1R0V

Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21212 space group

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)
A	d1r0va1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	tRNA-intron endonuclease catalytic domain-like	tRNA-intron endonuclease catalytic domain-like	Dimeric tRNA splicing endonuclease, domains 2 and 4	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
A	d1r0va3	Alpha and beta proteins (a+b)	MutS N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	Dimeric tRNA splicing endonuclease, domains 1 and 3	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
B	d1r0vb1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	tRNA-intron endonuclease catalytic domain-like	tRNA-intron endonuclease catalytic domain-like	Dimeric tRNA splicing endonuclease, domains 2 and 4	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
B	d1r0vb3	Alpha and beta proteins (a+b)	MutS N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	Dimeric tRNA splicing endonuclease, domains 1 and 3	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
C	d1r0vc1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	tRNA-intron endonuclease catalytic domain-like	tRNA-intron endonuclease catalytic domain-like	Dimeric tRNA splicing endonuclease, domains 2 and 4	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
C	d1r0vc3	Alpha and beta proteins (a+b)	MutS N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	Dimeric tRNA splicing endonuclease, domains 1 and 3	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
D	d1r0vd1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	tRNA-intron endonuclease catalytic domain-like	tRNA-intron endonuclease catalytic domain-like	Dimeric tRNA splicing endonuclease, domains 2 and 4	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
D	d1r0vd3	Alpha and beta proteins (a+b)	MutS N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	Dimeric tRNA splicing endonuclease, domains 1 and 3	(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)
A	SCOP2 Family	tRNA-intron endonuclease N-terminal domain-like	8027793	4001488	SCOP2 (2022-06-29)
A	SCOP2 Family	Sen15-like	8027789	4000499	SCOP2 (2022-06-29)
A	SCOP2 Family	Sen15-like	8027791	4000499	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	tRNA-intron endonuclease N-terminal domain-like	8040172	3001683	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	tRNA-intron endonuclease catalytic domain-like	8040168	3000437	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	tRNA-intron endonuclease catalytic domain-like	8040170	3000437	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8040170	3000437	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	tRNA-intron endonuclease N-terminal domain-like	8040172	3001683	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8040168	3000437	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8040168	3000437	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8040170	3000437	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	tRNA-intron endonuclease N-terminal domain-like	8040172	3001683	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8040168	3000437	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8040170	3000437	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	tRNA-intron endonuclease N-terminal domain-like	8040172	3001683	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	PF02778	e1r0vA1	A: a+b two layers	X: Homing endonucleases-like	H: tRNA-intron endonuclease N-terminal domain-like (From Topology)	T: tRNA-intron endonuclease N-terminal domain-like	F: PF02778	ECOD (1.6)
A	F_UNCLASSIFIED	e1r0vA2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: tRNA-intron endonuclease catalytic domain-like (From Topology)	T: tRNA-intron endonuclease catalytic domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF01974	e1r0vA3	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: tRNA-intron endonuclease catalytic domain-like (From Topology)	T: tRNA-intron endonuclease catalytic domain-like	F: PF01974	ECOD (1.6)
B	PF02778	e1r0vB1	A: a+b two layers	X: Homing endonucleases-like	H: tRNA-intron endonuclease N-terminal domain-like (From Topology)	T: tRNA-intron endonuclease N-terminal domain-like	F: PF02778	ECOD (1.6)
B	F_UNCLASSIFIED	e1r0vB2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: tRNA-intron endonuclease catalytic domain-like (From Topology)	T: tRNA-intron endonuclease catalytic domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF01974	e1r0vB3	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: tRNA-intron endonuclease catalytic domain-like (From Topology)	T: tRNA-intron endonuclease catalytic domain-like	F: PF01974	ECOD (1.6)
C	PF02778	e1r0vC1	A: a+b two layers	X: Homing endonucleases-like	H: tRNA-intron endonuclease N-terminal domain-like (From Topology)	T: tRNA-intron endonuclease N-terminal domain-like	F: PF02778	ECOD (1.6)
C	F_UNCLASSIFIED	e1r0vC2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: tRNA-intron endonuclease catalytic domain-like (From Topology)	T: tRNA-intron endonuclease catalytic domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF01974	e1r0vC3	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: tRNA-intron endonuclease catalytic domain-like (From Topology)	T: tRNA-intron endonuclease catalytic domain-like	F: PF01974	ECOD (1.6)
D	PF02778	e1r0vD1	A: a+b two layers	X: Homing endonucleases-like	H: tRNA-intron endonuclease N-terminal domain-like (From Topology)	T: tRNA-intron endonuclease N-terminal domain-like	F: PF02778	ECOD (1.6)
D	F_UNCLASSIFIED	e1r0vD2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: tRNA-intron endonuclease catalytic domain-like (From Topology)	T: tRNA-intron endonuclease catalytic domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF01974	e1r0vD3	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: tRNA-intron endonuclease catalytic domain-like (From Topology)	T: tRNA-intron endonuclease catalytic domain-like	F: PF01974	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
A	3.40.1170.20	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I	tRNA intron endonuclease, N-terminal domain	CATH (4.3.0)
B	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
B	3.40.1170.20	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I	tRNA intron endonuclease, N-terminal domain	CATH (4.3.0)
C	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
C	3.40.1170.20	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I	tRNA intron endonuclease, N-terminal domain	CATH (4.3.0)
D	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
D	3.40.1170.20	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I	tRNA intron endonuclease, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02778	tRNA intron endonuclease, N-terminal domain (tRNA_int_endo_N)	tRNA intron endonuclease, N-terminal domain	Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.	Domain
A, B, C, D	PF01974	tRNA intron endonuclease, catalytic C-terminal domain (tRNA_int_endo)	tRNA intron endonuclease, catalytic C-terminal domain	Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	tRNA-intron endonuclease	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters tRNA-specific ribonuclease activity endonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity, acting on a tRNA RNA endonuclease activity, producing 3'-phosphomonoesters tRNA-intron endonuclease activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity catalytic activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters tRNA-specific ribonuclease activity endonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity, acting on a tRNA RNA endonuclease activity, producing 3'-phosphomonoesters tRNA-intron endonuclease activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity catalytic activity lyase activity binding organic cyclic compound binding nucleic acid binding	RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation organic cyclic compound metabolic process organic substance metabolic process biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation organic cyclic compound metabolic process organic substance metabolic process biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation tRNA processing organic substance biosynthetic process nucleic acid catabolic process metabolic process cellular process RNA processing macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006677	tRNA intron endonuclease, catalytic domain-like	Domain
A, B, C, D	IPR036740	tRNA intron endonuclease, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR023516	tRNA-splicing endonuclease, archaeal long subfamily	Family
A, B, C, D	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR036167	tRNA intron endonuclease, catalytic domain-like superfamily	Homologous Superfamily
A, B, C, D	IPR006678	tRNA intron endonuclease, N-terminal	Domain
A, B, C, D	IPR006676	tRNA-splicing endonuclease	Family

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 R01GM133198.