7ZRZ

Structure of the human tRNA splicing endonuclease defines substrate recognition

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth DP1]	SCOP2B Superfamily	tRNA-intron endonuclease catalytic domain-like	8034132	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)
B [auth BP4]	PF01974	e7zrzBP41	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 [auth DP1]	PF09631	e7zrzDP11	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: PF09631	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AP1]	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
C [auth CP1]	PF12928	tRNA-splicing endonuclease subunit sen54 N-term (tRNA_int_end_N2)	tRNA-splicing endonuclease subunit sen54 N-term	This is an N-terminal family of archaeal and metazoan sen54 proteins that forms one of the tRNA-splicing endonuclease subunits.	Domain
D [auth DP1]	PF09631	Sen15 protein (Sen15)	Sen15 protein	The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this hetero-tetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a m ...	The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this hetero-tetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AP1]	tRNA-splicing endonuclease subunit Sen34	binding organic cyclic compound 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 binding organic cyclic compound 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	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process tRNA splicing, via endonucleolytic cleavage and ligation organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing RNA splicing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process tRNA splicing, via endonucleolytic cleavage and ligation organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing RNA splicing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process tRNA-type intron splice site recognition and cleavage biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex catalytic complex nuclear protein-containing complex endonuclease complex endoribonuclease complex intracellular protein-containing complex tRNA-intron endonuclease complex nucleoplasm
B [auth BP4]	tRNA-splicing endonuclease subunit Sen2	binding organic cyclic compound 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 binding organic cyclic compound 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	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process tRNA splicing, via endonucleolytic cleavage and ligation organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing RNA splicing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process tRNA splicing, via endonucleolytic cleavage and ligation organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing RNA splicing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process tRNA-type intron splice site recognition and cleavage biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cytoplasm cytosol protein-containing complex catalytic complex nuclear protein-containing complex endonuclease complex endoribonuclease complex intracellular protein-containing complex tRNA-intron endonuclease complex nucleoplasm
C [auth CP1]	tRNA-splicing endonuclease subunit Sen54	-	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process tRNA splicing, via endonucleolytic cleavage and ligation organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing RNA splicing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process tRNA splicing, via endonucleolytic cleavage and ligation organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing RNA splicing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process tRNA-type intron splice site recognition and cleavage biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex catalytic complex nuclear protein-containing complex endonuclease complex endoribonuclease complex intracellular protein-containing complex tRNA-intron endonuclease complex nucleoplasm
D [auth DP1]	tRNA-splicing endonuclease subunit Sen15	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 mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nucleoplasm
E [auth ZN1]	pre-tRNA Arg TCT 3-2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AP1]	IPR006677	tRNA intron endonuclease, catalytic domain-like	Domain
A [auth AP1]	IPR016690	tRNA-splicing endonuclease, SEN34 subunit	Family
A [auth AP1]	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
A [auth AP1]	IPR036167	tRNA intron endonuclease, catalytic domain-like superfamily	Homologous Superfamily
A [auth AP1]	IPR006676	tRNA-splicing endonuclease	Family
B [auth BP4]	IPR006677	tRNA intron endonuclease, catalytic domain-like	Domain
B [auth BP4]	IPR006678	tRNA intron endonuclease, N-terminal	Domain
B [auth BP4]	IPR016589	tRNA-splicing endonuclease, SEN2 subunit	Family
B [auth BP4]	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
B [auth BP4]	IPR036167	tRNA intron endonuclease, catalytic domain-like superfamily	Homologous Superfamily
B [auth BP4]	IPR006676	tRNA-splicing endonuclease	Family
C [auth CP1]	IPR024336	tRNA-splicing endonuclease, subunit Sen54, N-terminal	Domain
C [auth CP1]	IPR024337	tRNA-splicing endonuclease, subunit Sen54	Family
D [auth DP1]	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
D [auth DP1]	IPR036167	tRNA intron endonuclease, catalytic domain-like superfamily	Homologous Superfamily
D [auth DP1]	IPR018593	tRNA-splicing endonuclease subunit Sen15	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth AP1]	Pharos: Q9BSV6	pontocerebellar hypoplasia type 2C microcephaly intellectual disability pontocerebellar hypoplasia vision disorder Deglutition Disorders neurodegenerative disease alcoholic liver cirrhosis movement disorder pontocerebellar hypoplasia type 2 prostate carcinoma arthrogryposis Takayasu arteritis atypical teratoid rhabdoid tumor glioblastoma pontocerebellar hypoplasia type 2C microcephaly intellectual disability pontocerebellar hypoplasia vision disorder Deglutition Disorders neurodegenerative disease alcoholic liver cirrhosis movement disorder pontocerebellar hypoplasia type 2 prostate carcinoma arthrogryposis Takayasu arteritis atypical teratoid rhabdoid tumor glioblastoma microlissencephaly ovarian cancer psoriasis astrocytic tumor malignant glioma
B [auth BP4]	Pharos: Q8NCE0	pontocerebellar hypoplasia type 2B intellectual disability microcephaly Weight Gain pontocerebellar hypoplasia vision disorder movement disorder non-alcoholic fatty liver disease pancreatic intraductal papillary-mucinous neoplasm arthrogryposis lung cancer malignant mesothelioma microlissencephaly medulloblastoma neurodegenerative disease pontocerebellar hypoplasia type 2B intellectual disability microcephaly Weight Gain pontocerebellar hypoplasia vision disorder movement disorder non-alcoholic fatty liver disease pancreatic intraductal papillary-mucinous neoplasm arthrogryposis lung cancer malignant mesothelioma microlissencephaly medulloblastoma neurodegenerative disease osteosarcoma pontocerebellar hypoplasia type 2 malignant colon neoplasm
C [auth CP1]	Pharos: Q7Z6J9	pontocerebellar hypoplasia type 2A pontocerebellar hypoplasia type 4 pontocerebellar hypoplasia type 5 intellectual disability microcephaly pontocerebellar hypoplasia Deglutition Disorders vision disorder neurodegenerative disease arthrogryposis movement disorder pontocerebellar hypoplasia type 1 rhabdomyolysis large cell medulloblastoma microlissencephaly pontocerebellar hypoplasia type 2A pontocerebellar hypoplasia type 4 pontocerebellar hypoplasia type 5 intellectual disability microcephaly pontocerebellar hypoplasia Deglutition Disorders vision disorder neurodegenerative disease arthrogryposis movement disorder pontocerebellar hypoplasia type 1 rhabdomyolysis large cell medulloblastoma microlissencephaly osteosarcoma pontocerebellar hypoplasia type 2
D [auth DP1]	Pharos: Q8WW01	pontocerebellar hypoplasia, type 2F adrenoleukodystrophy Cerebellar Hypoplasia osteoarthritis pancreatic intraductal papillary-mucinous neoplasm pontocerebellar hypoplasia type 2 progressive supranuclear palsy atypical teratoid rhabdoid tumor glioblastoma osteosarcoma Pick disease breast cancer large cell medulloblastoma ovarian cancer pontocerebellar hypoplasia pontocerebellar hypoplasia, type 2F adrenoleukodystrophy Cerebellar Hypoplasia osteoarthritis pancreatic intraductal papillary-mucinous neoplasm pontocerebellar hypoplasia type 2 progressive supranuclear palsy atypical teratoid rhabdoid tumor glioblastoma osteosarcoma Pick disease breast cancer large cell medulloblastoma ovarian cancer pontocerebellar hypoplasia primitive neuroectodermal tumor

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.