8CBM | pdb_00008cbm

Structure of human mitochondrial CCA-adding enzyme in complex with mitochondrial pre-tRNA-Ile

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)
E	SCOP2B Superfamily	Nucleotidyltransferase-like	8034367	3000129	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Poly A polymerase C-terminal region-like	8034365	3001334	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F	PF01746	tRNA (Guanine-1)-methyltransferase TrmD (tRNA_m1G_MT)	tRNA (Guanine-1)-methyltransferase TrmD	-	Family
E	PF12627	Probable RNA and SrmB- binding site of polymerase A (PolyA_pol_RNAbd)	Probable RNA and SrmB- binding site of polymerase A	This region encompasses much of the RNA and SrmB binding motifs on polymerase A.	Domain
E	PF01743	Poly A polymerase head domain (PolyA_pol)	Poly A polymerase head domain	This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25 ...	This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25. This family is part of the nucleotidyltransferase superfamily.	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-Ile(0,0)	-	-	-
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 tRNA threonylcarbamoyladenosine metabolic process 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	CCA tRNA nucleotidyltransferase 1, mitochondrial	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 cytidylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity nucleotidyltransferase activity catalytic activity CCA tRNA nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups identical protein binding protein binding protein homodimerization activity protein dimerization activity CCACCA tRNA nucleotidyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA binding tRNA binding nucleic acid binding cation binding metal ion binding	cellular component disassembly ribosome disassembly rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process cellular component organization organelle organization organelle disassembly biosynthetic process translational elongation cellular process cellular component disassembly ribosome disassembly rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process cellular component organization organelle organization organelle disassembly biosynthetic process translational elongation cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process protein metabolic process catabolic process RNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process tRNA metabolic process tRNA surveillance nucleic acid catabolic process RNA surveillance tRNA decay RNA catabolic process mitochondrial gene expression mitochondrial tRNA 3'-end processing RNA biosynthetic process nucleic acid biosynthetic process mitochondrial RNA processing tRNA processing RNA 3'-end processing RNA processing tRNA 3'-end processing mitochondrial tRNA processing nucleobase-containing compound biosynthetic process mitochondrial RNA metabolic process mitochondrial RNA 3'-end processing tRNA 3'-terminal CCA addition	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen mitochondrial matrix
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 (3S)-3-hydroxyacyl-CoA 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+) activity 17-beta-hydroxysteroid dehydrogenase (NAD+) activity cholate 7-alpha-dehydrogenase (NAD+) activity (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity RNA binding binding nucleic acid binding tRNA binding chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity ursodeoxycholate 7-beta-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 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 bile acid biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process bile acid metabolic process 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 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 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	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	IPR007356	tRNA (guanine(9)-N1)-methyltransferase, eukaryotic	Family
F	IPR025812	tRNA methyltransferase 10 homolog C, TRM10-type domain	Domain
E	IPR050264	Bacterial CCA-adding enzyme type 3 subfamily	Family
E	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
E	IPR002646	Poly A polymerase, head domain	Domain
E	IPR032828	tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain	Domain
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: Q96Q11	congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome retinitis pigmentosa and erythrocytic microcytosis retinitis pigmentosa acute myeloid leukemia hepatocellular carcinoma myopathy periodic fever syndrome cone-rod dystrophy juvenile dermatomyositis osteosarcoma retinal degeneration Sjogren syndrome Mitochondrial Diseases ovarian cancer
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.