3P1Z

Crystal structure of the Aperopyrum pernix RNA splicing endonuclease

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SEN2_like	e3p1zA2	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: SEN2_like	ECOD (1.6)
A	tRNA_int_endo	e3p1zA1	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)
I	SEN2_like	e3p1zI1	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: SEN2_like	ECOD (1.6)
I	tRNA_int_endo	e3p1zI2	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)
K	SEN2_like	e3p1zK1	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: SEN2_like	ECOD (1.6)
K	tRNA_int_endo	e3p1zK2	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	SEN2_like	e3p1zC1	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: SEN2_like	ECOD (1.6)
C	tRNA_int_endo	e3p1zC2	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)
E	SEN2_like	e3p1zE1	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: SEN2_like	ECOD (1.6)
E	tRNA_int_endo	e3p1zE2	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)
G	SEN2_like	e3p1zG1	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: SEN2_like	ECOD (1.6)
G	tRNA_int_endo	e3p1zG2	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_N	e3p1zB2	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	ECOD (1.6)
B	tRNA_int_endo	e3p1zB1	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_N	e3p1zD1	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	ECOD (1.6)
D	tRNA_int_endo	e3p1zD2	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)
F	tRNA_int_endo_N	e3p1zF1	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	ECOD (1.6)
F	tRNA_int_endo	e3p1zF2	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)
H	tRNA_int_endo_N	e3p1zH1	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	ECOD (1.6)
H	tRNA_int_endo	e3p1zH2	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)
J	tRNA_int_endo_N	e3p1zJ1	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	ECOD (1.6)
J	tRNA_int_endo	e3p1zJ2	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)
L	tRNA_int_endo_N	e3p1zL1	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	ECOD (1.6)
L	tRNA_int_endo	e3p1zL2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
I	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)
I	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
K	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)
K	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)
C	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
E	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)
E	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
G	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)
G	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)
B	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)
D	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
F	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)
F	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
H	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)
H	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
J	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)
J	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
L	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)
L	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, C, E, G, I A, C, E, G, I, K	PF22502	tRNA-intron endonuclease SEN2-like, N-terminal domain (SEN2-like_N)	tRNA-intron endonuclease SEN2-like, N-terminal domain	This entry represents a tRNA-intron endonuclease SEN2-like N-terminal domain in a splicing endonuclease from Aeropyrum pernix [1,2].	Domain
A, C, E, G, I A, C, E, G, I, K	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
B, D, F, H, J B, D, F, H, J, L	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
B, D, F, H, J B, D, F, H, J, L	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, C, E, G, I A, C, E, G, I, K	Putative uncharacterized protein	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 binding organic cyclic compound binding nucleic acid binding	RNA splicing cellular biosynthetic process cellular metabolic process 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 cellular biosynthetic process cellular metabolic process 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	membrane cellular anatomical entity
B, D, F, H, J B, D, F, H, J, L	tRNA-splicing 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 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 tRNA-type intron splice site recognition and cleavage RNA splicing cellular biosynthetic process cellular metabolic process 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 tRNA-type intron splice site recognition and cleavage biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation tRNA processing metabolic process cellular process RNA processing macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR006677	tRNA intron endonuclease, catalytic domain-like	Domain
A, C, E, G, I A, C, E, G, I, K	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR036167	tRNA intron endonuclease, catalytic domain-like superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR006677	tRNA intron endonuclease, catalytic domain-like	Domain
B, D, F, H, J B, D, F, H, J, L	IPR036740	tRNA intron endonuclease, N-terminal domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR036167	tRNA intron endonuclease, catalytic domain-like superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR006678	tRNA intron endonuclease, N-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR006676	tRNA-splicing endonuclease	Family
B, D, F, H, J B, D, F, H, J, L	IPR016442	tRNA-splicing endonuclease, archaeal short subfamily	Family