Annotations: 8HMZ

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	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)
G [auth E]	F_UNCLASSIFIED	e8hmzE3	A: beta barrels	X: Protein CLP1 C-terminal domain (From Topology)	H: Protein CLP1 C-terminal domain (From Topology)	T: Protein CLP1 C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
G [auth E]	F_UNCLASSIFIED	e8hmzE2	A: beta sandwiches	X: jelly-roll	H: Protein CLP1 jelly-roll domain (From Topology)	T: Protein CLP1 jelly-roll domain	F: F_UNCLASSIFIED	ECOD (1.6)
G [auth E]	F_UNCLASSIFIED	e8hmzE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e8hmzD1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	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
G [auth E]	PF06807	Pre-mRNA cleavage complex II protein Clp1 (Clp1)	Pre-mRNA cleavage complex II protein Clp1	-	Family
G [auth E]	PF16573	N-terminal beta-sandwich domain of polyadenylation factor (CLP1_N)	N-terminal beta-sandwich domain of polyadenylation factor	-	Family
G [auth E]	PF16575	mRNA cleavage and polyadenylation factor CLP1 P-loop (CLP1_P)	mRNA cleavage and polyadenylation factor CLP1 P-loop	CLP1_P is the P-loop carrying domain of Clp1 mRNA cleavage and polyadenylation factor, Clp1, proteins in eukaryotes. Clp1 is essential for 3'-end processing of mRNAs. This region carries the P-loop suggesting it is the region that binds adenine or g ...	CLP1_P is the P-loop carrying domain of Clp1 mRNA cleavage and polyadenylation factor, Clp1, proteins in eukaryotes. Clp1 is essential for 3'-end processing of mRNAs. This region carries the P-loop suggesting it is the region that binds adenine or guanine nucleotide [1].	Domain
D	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	tRNA-splicing endonuclease subunit Sen2	binding nucleic acid binding 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	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 tRNA-type intron splice site recognition and cleavage biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation 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 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 mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen 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
B	tRNA-splicing endonuclease subunit Sen34	binding nucleic acid binding 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	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 tRNA-type intron splice site recognition and cleavage biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation 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 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 mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex catalytic complex nuclear protein-containing complex endonuclease complex endoribonuclease complex intracellular protein-containing complex tRNA-intron endonuclease complex nucleoplasm
C	tRNA-splicing endonuclease subunit Sen54	-	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 tRNA-type intron splice site recognition and cleavage biosynthetic process RNA splicing, via endonucleolytic cleavage and ligation 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 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 mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex catalytic complex nuclear protein-containing complex endonuclease complex endoribonuclease complex intracellular protein-containing complex tRNA-intron endonuclease complex nucleoplasm
E [auth 5]	Pre-tRNA 5' END	-	-	-
F [auth 3]	Pre-tRNA 3' END	-	-	-
G [auth E]	Polyribonucleotide 5'-hydroxyl-kinase Clp1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding nucleobase-containing compound kinase activity polynucleotide 5'-hydroxyl-kinase activity kinase activity ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity transferase activity ATP-dependent polynucleotide 5'-hydroxyl-kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process developmental process multicellular organismal process head development animal organ development brain development nervous system development cerebellar cortex development multicellular organism development cerebellum development central nervous system development metencephalon development anatomical structure development hindbrain development system development regulation of cellular process negative regulation of biological process post-transcriptional regulation of gene expression negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of gene expression global gene silencing by mRNA cleavage negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of macromolecule biosynthetic process regulation of metabolic process ribonucleoprotein complex biogenesis RISC complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization regulatory ncRNA-mediated gene silencing RNA splicing tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation RNA splicing, via endonucleolytic cleavage and ligation tRNA processing	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex mRNA cleavage factor complex intracellular membrane-bounded organelle cytoplasm cytosol catalytic complex endonuclease complex membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex mRNA cleavage factor complex intracellular membrane-bounded organelle cytoplasm cytosol catalytic complex endonuclease complex endoribonuclease complex intracellular protein-containing complex tRNA-intron endonuclease complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
D	Chromosome 1 open reading frame 19, isoform CRA_a	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 mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006677	tRNA intron endonuclease, catalytic domain-like	Domain
A	IPR006678	tRNA intron endonuclease, N-terminal	Domain
A	IPR016589	tRNA-splicing endonuclease, SEN2 subunit	Family
A	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
A	IPR036167	tRNA intron endonuclease, catalytic domain-like superfamily	Homologous Superfamily
A	IPR006676	tRNA-splicing endonuclease	Family
B	IPR006677	tRNA intron endonuclease, catalytic domain-like	Domain
B	IPR016690	TSEN34	Family
B	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
B	IPR036167	tRNA intron endonuclease, catalytic domain-like superfamily	Homologous Superfamily
B	IPR006676	tRNA-splicing endonuclease	Family
C	IPR024336	tRNA-splicing endonuclease, subunit Sen54, N-terminal	Domain
C	IPR024337	tRNA-splicing endonuclease, subunit Sen54	Family
G [auth E]	IPR028606	Clp1	Family
G [auth E]	IPR038239	Clp1, N-terminal domain superfamily	Homologous Superfamily
G [auth E]	IPR038238	Clp1, C-terminal domain superfamily	Homologous Superfamily
G [auth E]	IPR032324	Clp1, N-terminal	Domain
G [auth E]	IPR032319	Clp1, P-loop domain	Domain
G [auth E]	IPR045116	Clp1/Grc3	Family
G [auth E]	IPR010655	Clp1, C-terminal	Domain
G [auth E]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D	IPR011856	tRNA endonuclease-like domain superfamily	Homologous Superfamily
D	IPR036167	tRNA intron endonuclease, catalytic domain-like superfamily	Homologous Superfamily
D	IPR018593	tRNA-splicing endonuclease subunit Sen15	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8NCE0	pontocerebellar hypoplasia type 2B intellectual disability microcephaly Deglutition Disorders 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 Deglutition Disorders 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
B	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 Takayasu arteritis arthrogryposis 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 Takayasu arteritis arthrogryposis atypical teratoid rhabdoid tumor glioblastoma microlissencephaly ovarian cancer psoriasis astrocytic tumor malignant glioma
C	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
G [auth E]	Pharos: Q92989	pontocerebellar hypoplasia type 10 Liver Cirrhosis, Experimental pontocerebellar hypoplasia endogenous depression lung cancer autism spectrum disorder intellectual disability neurodegenerative disease tuberculosis
D	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