8CBL

Structure of human mitochondrial RNase Z in complex with mitochondrial pre-tRNA-His(0,Ser)

External Resource: Annotation

Domain Annotation: SCOP2 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)
A	SCOP2B Superfamily	SDR-like	8058497	3000038	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	SDR-like	8058497	3000038	SCOP2B (2021-05-27)
C	SCOP2B Superfamily	SDR-like	8058497	3000038	SCOP2B (2021-05-27)
D	SCOP2B Superfamily	SDR-like	8058497	3000038	SCOP2B (2021-05-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00106	short chain dehydrogenase (adh_short)	short chain dehydrogenase	This family contains a wide variety of dehydrogenases.	Domain
E	PF13691	tRNase Z endonuclease (Lactamase_B_4)	tRNase Z endonuclease	This is family of tRNase Z enzymes, that are closely related structurally to the Lactamase_B family members. tRNase Z is the endonuclease that is involved in tRNA 3'-end maturation through removal of the 3'-trailer sequences from tRNA precursors. The ...	This is family of tRNase Z enzymes, that are closely related structurally to the Lactamase_B family members. tRNase Z is the endonuclease that is involved in tRNA 3'-end maturation through removal of the 3'-trailer sequences from tRNA precursors. The fission yeast Schizosaccharomyces pombe contains two candidate tRNase Zs encoded by two essential genes. The first, Swiss:Q10155, is targeted to the nucleus and has an SV40 nuclear localisation signal at its N-terminus, consisting of four consecutive arginine and lysine residues between residues 208 and 211 (KKRK) that is critical for the NLS function. The second, Swiss:P87168, is targeted to the mitochondria, with an N-terminal mitochondrial targeting signal within the first 38 residues [1].	Domain
E	PF12706	Beta-lactamase superfamily domain (Lactamase_B_2)	Beta-lactamase superfamily domain	This family is part of the beta-lactamase superfamily and is related to Pfam:PF00753.	Domain
F	PF01746	tRNA (Guanine-1)-methyltransferase (tRNA_m1G_MT)	tRNA (Guanine-1)-methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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(P)+] activity testosterone dehydrogenase (NAD+) activity 3-hydroxyacyl-CoA dehydrogenase activity 17-beta-hydroxysteroid dehydrogenase (NAD+) activity RNA binding 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(P)+] activity testosterone dehydrogenase (NAD+) activity 3-hydroxyacyl-CoA dehydrogenase activity 17-beta-hydroxysteroid dehydrogenase (NAD+) activity RNA binding binding organic cyclic compound binding nucleic acid binding tRNA binding chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity androstan-3-alpha,17-beta-diol dehydrogenase activity estradiol 17-beta-dehydrogenase [NAD(P)+] activity ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity cholate 7-alpha-dehydrogenase activity	regulation of hormone levels steroid metabolic process biological regulation androgen metabolic process primary metabolic process metabolic process regulation of biological quality hormone metabolic process lipid metabolic process catabolic process oxoacid metabolic process organic acid catabolic process organic acid metabolic process cellular lipid catabolic process regulation of hormone levels steroid metabolic process biological regulation androgen metabolic process primary metabolic process metabolic process regulation of biological quality hormone metabolic process lipid metabolic process catabolic process oxoacid metabolic process organic acid catabolic process organic acid metabolic process cellular lipid catabolic process cellular catabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation small molecule metabolic process lipid oxidation fatty acid metabolic process lipid catabolic process cellular metabolic process carboxylic acid metabolic process lipid modification fatty acid catabolic process cellular lipid metabolic process cellular process monocarboxylic acid metabolic process 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 cellular biosynthetic process 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 tRNA threonylcarbamoyladenosine metabolic process 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 organic hydroxy compound metabolic process lipid biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process steroid biosynthetic process bile acid biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process bile acid metabolic process organic hydroxy compound biosynthetic process steroid catabolic process amino acid metabolic process alpha-amino acid metabolic process branched-chain amino acid catabolic process branched-chain amino acid metabolic process isoleucine catabolic process amino acid catabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process alpha-amino acid catabolic process isoleucine metabolic process cellular 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	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane protein-containing complex catalytic complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol 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 nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle mitochondrial nucleoid non-membrane-bounded organelle
E	Zinc phosphodiesterase ELAC protein 2	endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity, acting on a tRNA nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 3'-tRNA processing endoribonuclease activity catalytic activity RNA binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity, acting on a tRNA nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 3'-tRNA processing endoribonuclease activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding tRNA-specific ribonuclease activity cation binding ion binding metal ion binding small molecule binding	cellular biosynthetic process mitochondrial tRNA processing cellular metabolic process 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 cellular biosynthetic process mitochondrial tRNA processing cellular metabolic process 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 catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process tRNA decay RNA catabolic process mitochondrial tRNA 3'-end processing RNA 3'-end processing tRNA 3'-end processing mitochondrial RNA 3'-end processing	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle mitochondrial nucleoid non-membrane-bounded organelle nucleus nucleoplasm nuclear lumen
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 organic cyclic compound binding nucleic acid binding tRNA binding tRNA (guanine) methyltransferase activity tRNA (guanosine(9)-N1)-methyltransferase activity identical protein binding protein binding	cellular biosynthetic process mitochondrial tRNA processing cellular metabolic process 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 cellular biosynthetic process mitochondrial tRNA processing cellular metabolic process 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 organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic 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 organonitrogen compound metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process translation regulation of cellular biosynthetic process 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 cellular biosynthetic 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 tRNA threonylcarbamoyladenosine metabolic process mitochondrial tRNA methylation tRNA modification macromolecule methylation RNA modification methylation macromolecule modification RNA methylation tRNA methylation	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle mitochondrial nucleoid non-membrane-bounded organelle 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
G [auth T]	Mitochondrial Precursor tRNA-His(0,Ser)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
E	IPR001279	Metallo-beta-lactamase	Domain
E	IPR047151	Zinc phosphodiesterase ELAC protein 2-like	Family
E	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
E	IPR027794	tRNase Z endonuclease	Domain
F	IPR007356	tRNA (guanine-N1-)-methyltransferase, eukaryotic	Family
F	IPR016009	tRNA methyltransferase TRMD/TRM10-type domain	Domain
F	IPR028564	tRNA methyltransferase TRM10-type domain	Domain
F	IPR038459	tRNA methyltransferase TRM10-type domain superfamily	Homologous Superfamily
F	IPR025812	tRNA methyltransferase 10 homolog C, TRM10-type domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
E	Pharos: Q9BQ52	prostate cancer familial prostate carcinoma prostate cancer, hereditary, 2 combined oxidative phosphorylation defect type 17 astrocytic tumor combined oxidative phosphorylation deficiency mitochondrial complex I deficiency cancer Mitochondrial Diseases intellectual disability ovarian cancer
F	Pharos: Q7L0Y3	combined oxidative phosphorylation defect type 30 breast cancer Mitochondrial Diseases

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.