8ORJ | pdb_00008orj

Cryo-EM structure of human tRNA ligase RTCB in complex with human PYROXD1.

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
B	PF18267	Rubredoxin NAD+ reductase C-terminal domain (Rubredoxin_C)	Rubredoxin NAD+ reductase C-terminal domain	This is the C-terminal domain of NADH rubredoxin oxidoreductase present in Clostridium acetobutylicum. The majority of obligatory anaerobes detoxify micro-aerobic environments by consuming O2 via H2O-forming NADH oxidase. This enzyme offers an altern ...	This is the C-terminal domain of NADH rubredoxin oxidoreductase present in Clostridium acetobutylicum. The majority of obligatory anaerobes detoxify micro-aerobic environments by consuming O2 via H2O-forming NADH oxidase. This enzyme offers an alternate reaction pathway for scavenging of O2 and reactive oxygen species, wherein the reducing equivalent is obtained from NADH [1].	Domain
A	PF01139	tRNA-splicing ligase RtcB (RtcB)	tRNA-splicing ligase RtcB	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1	NAD(P)H oxidase H2O2-forming activity oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor	cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular process cellular response to chemical stress	intracellular anatomical structure intracellular membraneless organelle sarcomere intracellular organelle cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex membrane-bounded organelle intracellular anatomical structure intracellular membraneless organelle sarcomere intracellular organelle cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A	RNA-splicing ligase RtcB homolog	cytoskeletal protein binding protein binding binding vinculin binding ligase activity, forming phosphoric ester bonds RNA ligase (GTP) activity catalytic activity, acting on RNA RNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity ligase activity RNA binding nucleic acid binding guanyl nucleotide binding cytoskeletal protein binding protein binding binding vinculin binding ligase activity, forming phosphoric ester bonds RNA ligase (GTP) activity catalytic activity, acting on RNA RNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity ligase activity RNA binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding	developmental process placenta development animal organ development anatomical structure development 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 developmental process placenta development animal organ development anatomical structure development 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 multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol tRNA-splicing ligase complex protein-containing complex membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol tRNA-splicing ligase complex protein-containing complex catalytic complex intracellular protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR041575	NADH-rubredoxin oxidoreductase, C-terminal	Domain
B	IPR050260	FAD-dependent oxidoreductase	Family
B	IPR023753	FAD/NAD(P)-binding domain	Domain
B	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily	Homologous Superfamily
B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR036025	tRNA-splicing ligase RtcB-like superfamily	Homologous Superfamily
A	IPR027513	RNA-splicing ligase RtcB homologue, eukaryotic	Family
A	IPR001233	RNA-splicing ligase, RtcB	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q8WU10	myofibrillar myopathy 8 myopathy myofibrillar myopathy astrocytic tumor muscle tissue disease Pick disease diabetes mellitus muscular disease progressive supranuclear palsy limb-girdle muscular dystrophy osteosarcoma psoriasis
A	Pharos: Q9Y3I0	acute myeloid leukemia lung cancer congestive heart failure pancreatic ductal adenocarcinoma diabetes mellitus primary cutaneous T-cell non-Hodgkin lymphoma

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.