7ONU | pdb_00007onu

Structure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-Tyr

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)
E	SCOP2B Superfamily	PIN domain-like	8095929	3001041	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ARM repeat-like	8095930	3000116	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SDR-like	8058497	3000038	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SDR-like	8058497	3000038	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SDR-like	8058497	3000038	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SDR-like	8058497	3000038	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)
F		e7onuF01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F:	ECOD (v294.1)
E	Lon_lid	e7onuE1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Lon_lid	ECOD (v294.1)
D	Trypsin	e7onuD1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin	ECOD (v294.1)
C	Trypsin	e7onuC1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin	ECOD (v294.1)
B	Trypsin	e7onuB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin	ECOD (v294.1)
A	F-actin_cap_A	e7onuA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: F-actin_cap_A	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF16953	Protein-only RNase P (PRORP)	Protein-only RNase P	PRORPs (protein-only RNase P) are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes [1]. Arabidopsis thaliana contains PRORP enzymes (PRORP1, PRORP2 and PRORP3) where PRORP1 localizes to mitocho ...	PRORPs (protein-only RNase P) are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes [1]. Arabidopsis thaliana contains PRORP enzymes (PRORP1, PRORP2 and PRORP3) where PRORP1 localizes to mitochondria as well as chloroplasts, while PRORP2 and PRORP3 are found in the nucleus. In humans and most other metazoans, mt-RNase P is composed of three protein subunits (mitochondrial RNase P proteins 1-3; MRPP1-3), homologs to the Arabidopsis thaliana PRORP1-3. This domain corresponds to the metallonuclease domain of PRORPs. PRORP1 has 22% sequence identity to the human homologue MRPP3. PRORP1 crystal structure shows a V-shaped tripartite structure with a C-terminal metallonuclease domain of the NYN (N4BL1, YacP-like nuclease) family, with a typical and functional two-metal-ion catalytic site that has conserved aspartate residues [2].	Domain
A, B, C, D	PF00106	short chain dehydrogenase (adh_short)	short chain dehydrogenase	This family contains a wide variety of dehydrogenases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth T]	Mitochondrial Precursor tRNA-Tyr	-	-	-
F	tRNA methyltransferase 10 homolog C	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (adenine) methyltransferase activity tRNA (adenine(9)-N1)-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (adenine) methyltransferase activity tRNA (adenine(9)-N1)-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding nucleic acid binding tRNA binding tRNA (guanine) methyltransferase activity tRNA (guanosine(9)-N1)-methyltransferase activity identical protein binding protein binding	mitochondrial tRNA processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mitochondrial gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process tRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process mitochondrial RNA processing biosynthetic process tRNA processing mitochondrial tRNA processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mitochondrial gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process tRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process mitochondrial RNA processing biosynthetic process tRNA processing metabolic process cellular process mitochondrial RNA metabolic process macromolecule metabolic process RNA processing mitochondrial tRNA 5'-end processing tRNA 5'-end processing mitochondrial RNA 5'-end processing RNA 5'-end processing regulation of cellular process mitochondrial translation positive regulation of protein metabolic process regulation of mitochondrial gene expression positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation regulation of gene expression positive regulation of gene expression regulation of mitochondrial translation regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of mitochondrial translation mitochondrial tRNA 3'-end processing RNA 3'-end processing tRNA 3'-end processing mitochondrial RNA 3'-end processing mitochondrial tRNA modification mitochondrial RNA modification mitochondrial tRNA methylation tRNA modification macromolecule methylation RNA modification methylation macromolecule modification RNA methylation tRNA methylation mRNA processing mRNA metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membraneless organelle mitochondrial nucleoid protein-containing complex catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex nucleus nucleoplasm nuclear lumen mitochondrial protein-containing complex ribonuclease P complex endonuclease complex endoribonuclease complex ribonucleoprotein complex mitochondrial ribonuclease P complex intracellular protein-containing complex
E	Mitochondrial ribonuclease P catalytic subunit	tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity, acting on a tRNA hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity ribonuclease P activity catalytic activity cation binding tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity, acting on a tRNA hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity ribonuclease P activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	mitochondrial tRNA 5'-end processing RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process mitochondrial RNA processing tRNA processing RNA processing tRNA 5'-end processing mitochondrial tRNA processing primary metabolic process mitochondrial RNA 5'-end processing gene expression mitochondrial tRNA 5'-end processing RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process mitochondrial RNA processing tRNA processing RNA processing tRNA 5'-end processing mitochondrial tRNA processing primary metabolic process mitochondrial RNA 5'-end processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process biosynthetic process RNA 5'-end processing metabolic process cellular process mitochondrial RNA metabolic process macromolecule metabolic process tRNA 5'-leader removal	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membraneless organelle mitochondrial nucleoid nucleus nucleoplasm nuclear lumen mitochondrial protein-containing complex protein-containing complex catalytic complex ribonuclease P complex endonuclease complex endoribonuclease complex ribonucleoprotein complex mitochondrial ribonuclease P complex intracellular protein-containing complex
A, B, C, D	3-hydroxyacyl-CoA dehydrogenase type-2	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity catalytic activity steroid dehydrogenase activity steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity testosterone dehydrogenase (NAD+) activity 17-beta-hydroxysteroid dehydrogenase (NAD+) activity cholate 7-alpha-dehydrogenase (NAD+) activity RNA binding binding nucleic acid binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity catalytic activity steroid dehydrogenase activity steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity testosterone dehydrogenase (NAD+) activity 17-beta-hydroxysteroid dehydrogenase (NAD+) activity cholate 7-alpha-dehydrogenase (NAD+) activity RNA binding binding nucleic acid binding tRNA binding chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity cardiolipin dehydrogenase (NAD+) activity estradiol 17-beta-dehydrogenase [NAD(P)+] activity	regulation of hormone levels steroid metabolic process biological regulation androgen metabolic process primary metabolic process metabolic process cellular process regulation of biological quality hormone metabolic process lipid metabolic process fatty acid metabolic process lipid catabolic process catabolic process oxoacid metabolic process regulation of hormone levels steroid metabolic process biological regulation androgen metabolic process primary metabolic process metabolic process cellular process regulation of biological quality hormone metabolic process lipid metabolic process fatty acid metabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process lipid modification organic acid metabolic process organic acid catabolic process fatty acid catabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation small molecule metabolic process monocarboxylic acid metabolic process lipid oxidation small molecule catabolic process estrogen metabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis mitochondrial tRNA modification RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process mitochondrial RNA processing tRNA processing mitochondrial RNA modification RNA processing mitochondrial tRNA methylation mitochondrial tRNA processing tRNA modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA modification biosynthetic process methylation macromolecule modification macromolecule metabolic process mitochondrial RNA metabolic process RNA methylation tRNA methylation bile acid biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process bile acid metabolic process ketone metabolic process brexanolone metabolic process C21-steroid hormone metabolic process mitochondrial tRNA 5'-end processing tRNA 5'-end processing mitochondrial RNA 5'-end processing RNA 5'-end processing mitochondrial tRNA 3'-end processing RNA 3'-end processing tRNA 3'-end processing mitochondrial RNA 3'-end processing organelle organization mitochondrion organization amino acid metabolic process alpha-amino acid metabolic process branched-chain amino acid catabolic process L-isoleucine catabolic process branched-chain amino acid metabolic process amino acid catabolic process L-amino acid catabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process isoleucine metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex catalytic complex methyltransferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex mitochondrial protein-containing complex ribonuclease P complex endonuclease complex endoribonuclease complex ribonucleoprotein complex mitochondrial ribonuclease P complex intracellular protein-containing complex membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membraneless organelle mitochondrial nucleoid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F	IPR028564	tRNA methyltransferase TRM10-type domain	Domain
F	IPR038459	tRNA methyltransferase TRM10-type domain superfamily	Homologous Superfamily
F	IPR007356	tRNA (guanine(9)-N1)-methyltransferase, eukaryotic	Family
F	IPR025812	tRNA methyltransferase 10 homolog C, TRM10-type domain	Domain
E	IPR033495	Mitochondrial ribonuclease P catalytic subunit, PIN domain	Domain
E	IPR031595	Protein-only RNase P, C-terminal	Domain
E	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A, B, C, D	IPR002347	Short-chain dehydrogenase/reductase SDR	Family
A, B, C, D	IPR020904	Short-chain dehydrogenase/reductase, conserved site	Conserved Site
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
F	Pharos: Q7L0Y3	combined oxidative phosphorylation defect type 30 breast cancer Mitochondrial Diseases
E	Pharos: O15091	psoriasis atopic eczema osteosarcoma
A, B, C, D	Pharos: Q99714	HSD10 mitochondrial disease intellectual disability 2-methyl-3-hydroxybutyric aciduria chromosome Xp11.22 duplication syndrome lung adenocarcinoma neurodegenerative disease

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.