Annotations: 1A79

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1a79a1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	tRNA-intron endonuclease catalytic domain-like	tRNA-intron endonuclease catalytic domain-like	Tetrameric tRNA splicing endonuclease, C-terminal domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A	d1a79a2	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	Tetrameric tRNA splicing endonuclease, N-terminal domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1a79b1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	tRNA-intron endonuclease catalytic domain-like	tRNA-intron endonuclease catalytic domain-like	Tetrameric tRNA splicing endonuclease, C-terminal domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1a79b2	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	Tetrameric tRNA splicing endonuclease, N-terminal domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1a79c1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	tRNA-intron endonuclease catalytic domain-like	tRNA-intron endonuclease catalytic domain-like	Tetrameric tRNA splicing endonuclease, C-terminal domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1a79c2	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	Tetrameric tRNA splicing endonuclease, N-terminal domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d1a79d1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	tRNA-intron endonuclease catalytic domain-like	tRNA-intron endonuclease catalytic domain-like	Tetrameric tRNA splicing endonuclease, C-terminal domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d1a79d2	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	Tetrameric tRNA splicing endonuclease, N-terminal domain	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	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	8023538	4001488	SCOP2 (2022-06-29)
A	SCOP2 Family	Sen15-like	8032073	4000499	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	tRNA-intron endonuclease N-terminal domain-like	8035918	3001683	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	tRNA-intron endonuclease catalytic domain-like	8044451	3000437	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8044451	3000437	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	tRNA-intron endonuclease N-terminal domain-like	8035918	3001683	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	tRNA-intron endonuclease N-terminal domain-like	8035918	3001683	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8044451	3000437	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	tRNA-intron endonuclease N-terminal domain-like	8035918	3001683	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8044451	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)
A	tRNA_int_endo_N	e1a79A1	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)
A	tRNA_int_endo	e1a79A2	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	e1a79B1	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	e1a79B2	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_N	e1a79C1	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)
C	tRNA_int_endo	e1a79C2	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	e1a79D1	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	e1a79D2	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	3.40.1350.10	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 ENDONUCLEASE	binding nucleic acid binding 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 binding nucleic acid binding 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	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process macromolecule metabolic process RNA processing RNA splicing tRNA splicing, via endonucleolytic cleavage and ligation RNA splicing, via endonucleolytic cleavage and ligation	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	IPR006678	tRNA intron endonuclease, N-terminal	Domain
A, B, C, D	IPR016442	tRNA-splicing endonuclease, archaeal short 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	IPR006676	tRNA-splicing endonuclease	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	tRNA-intron lyase M-CSA #565	RNA endonuclease from the archaea Methanocaldococcus jannaschii is able to catalyse the splicing of introns from tRNA, a process needed only in archaea and eukarya, bacterial tRNA introns being self-splicing. The enzyme thus is a homologue of the eukaryotic enzymes which perform, a fact that serves to reinforce the closer relationship proposed between archaea and eukarya. There are differences however in the exact orientation of residues at the active site and the substrate recognition by the enzymes, suggesting that the enzymes evolved from a common ancestor with slightly different function.	Defined by 3 residues: TYR:A-107 [auth A-115]HIS:A-117 [auth A-125]LYS:A-148 [auth A-156] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.6.1.16 (UniProt) Search M-CSA Motif + EC 4.6.1.16

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.