4XGL | pdb_00004xgl

Structure of the nuclease subunit of human mitochondrial RNase P (MRPP3) at 1.8A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2 Family	PRORP catalytic domain-like	8046384	4005054	SCOP2 (2022-06-29)
A	SCOP2 Family	PRORP substrate-binding domain-like	8095928	4005164	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PIN domain-like	8095929	3001041	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ARM repeat-like	8095930	3000116	SCOP2 (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	EUF08222	e4xglA5	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: EUF08222	ECOD (1.6)
A	RNase_Zc3h12a	e4xglA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: RNase_Zc3h12a	ECOD (1.6)
A	PRORP_N	e4xglA4	A: few secondary structure elements	X: Protein-only RNase P Zn-binding domain (From Topology)	H: Protein-only RNase P Zn-binding domain (From Topology)	T: Protein-only RNase P Zn-binding domain	F: PRORP_N	ECOD (1.6)
A	PRORP_C	e4xglA3	A: few secondary structure elements	X: Protein-only RNase P Zn-binding domain (From Topology)	H: Protein-only RNase P Zn-binding domain (From Topology)	T: Protein-only RNase P Zn-binding domain	F: PRORP_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.11980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Mitochondrial ribonuclease P protein 3	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR033495	Mitochondrial ribonuclease P catalytic subunit, PIN domain	Domain
A	IPR031595	Protein-only RNase P, C-terminal	Domain
A	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O15091	psoriasis atopic eczema osteosarcoma

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.