3P1Y | pdb_00003p1y

Crystal structure of the chimeric Archaeoglobus fulgidus RNA splicing endonuclease with the broadest substrate specificity

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)
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)
D	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)
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)
B	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8040170	3000437	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8040168	3000437	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	tRNA-intron endonuclease N-terminal domain-like	8040172	3001683	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8040170	3000437	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)
D	tRNA_int_endo_N_1	e3p1yD1	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: tRNA_int_endo_N_1	ECOD (1.6)
D	tRNA_int_endo	e3p1yD4	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: tRNA_int_endo	ECOD (1.6)
D	tRNA_int_endo_1	e3p1yD5	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: tRNA_int_endo_1	ECOD (1.6)
C	tRNA_int_endo_N_1	e3p1yC4	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: tRNA_int_endo_N_1	ECOD (1.6)
C	tRNA_int_endo	e3p1yC2	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: tRNA_int_endo	ECOD (1.6)
C	tRNA_int_endo_1	e3p1yC1	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: tRNA_int_endo_1	ECOD (1.6)
B	tRNA_int_endo_N_1	e3p1yB4	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: tRNA_int_endo_N_1	ECOD (1.6)
B	tRNA_int_endo	e3p1yB2	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: tRNA_int_endo	ECOD (1.6)
B	tRNA_int_endo_1	e3p1yB1	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: tRNA_int_endo_1	ECOD (1.6)
A	tRNA_int_endo_N_1	e3p1yA4	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: tRNA_int_endo_N_1	ECOD (1.6)
A	tRNA_int_endo	e3p1yA2	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: tRNA_int_endo	ECOD (1.6)
A	tRNA_int_endo_1	e3p1yA1	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: tRNA_int_endo_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.1350.150	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)
D	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
C	3.40.1350.150	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)
C	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
B	3.40.1350.150	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)
B	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
A	3.40.1350.150	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)
A	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	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-splicing endonuclease	tRNA-specific ribonuclease activity endonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity, acting on a tRNA tRNA-intron lyase activity phosphorus-oxygen lyase activity nuclease activity RNA endonuclease activity lyase activity catalytic activity binding nucleic acid binding	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation nucleic acid biosynthetic process biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation tRNA processing RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation nucleic acid biosynthetic process biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation tRNA processing metabolic process cellular process RNA processing macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

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
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	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
A, B, C, D	IPR016442	tRNA-splicing endonuclease, archaeal short subfamily	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 R01GM157729.