9O4M | pdb_00009o4m

Crystal structure of Ubiquitin Carboxy Terminal Hydrolase L1 Q209C mutant covalently crosslinked to ubiquitin genetically encoded with N6-(6-bromohexanoyl)-L-lysine

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)
D [auth B]	SCOP2B Superfamily	Cysteine proteinases	8040164	3001808	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Cysteine proteinases	8040164	3001808	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF01088	Ubiquitin carboxyl-terminal hydrolase, family 1 (Peptidase_C12)	Ubiquitin carboxyl-terminal hydrolase, family 1		Domain
A [auth C], B [auth D]	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth B]	Ubiquitin carboxyl-terminal hydrolase isozyme L1	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity protein binding binding ubiquitin binding ubiquitin-like protein binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity protein binding binding ubiquitin binding ubiquitin-like protein binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity ribonucleoprotein complex binding protein-containing complex binding ribosome binding adrenergic receptor binding signaling receptor binding G protein-coupled receptor binding alpha-2A adrenergic receptor binding molecular function inhibitor activity molecular function regulator activity signaling receptor inhibitor activity signaling receptor regulator activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport axonal transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated axo-dendritic transport mitochondrion transport along microtubule organelle localization establishment of localization in cell establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport axonal transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated axo-dendritic transport mitochondrion transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement microtubule-based process axonal transport of mitochondrion ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration regulation of cellular process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process regulation of generation of precursor metabolites and energy positive regulation of phosphate metabolic process nucleoside phosphate catabolic process organic acid metabolic process regulation of primary metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of purine nucleotide catabolic process positive regulation of nucleotide catabolic process regulation of small molecule metabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process regulation of biological process positive regulation of phosphorus metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process positive regulation of ATP metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process metabolic process regulation of phosphorus metabolic process regulation of nucleotide catabolic process positive regulation of carbohydrate metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process regulation of metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process catabolic process energy derivation by oxidation of organic compounds positive regulation of nucleotide metabolic process positive regulation of purine nucleotide catabolic process positive regulation of biological process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process positive regulation of cellular process nucleotide catabolic process purine nucleoside triphosphate metabolic process carbohydrate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process positive regulation of glycolytic process biological regulation ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy regulation of catabolic process regulation of glycolytic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of catabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process positive regulation of small molecule metabolic process purine ribonucleoside diphosphate catabolic process macroautophagy autophagy regulation of autophagy regulation of macroautophagy process utilizing autophagic mechanism response to stimulus response to stress response to ischemia protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process behavior multicellular organismal process eating behavior feeding behavior system process nervous system process neuromuscular process proteolysis involved in protein catabolic process proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process germ cell proliferation cell population proliferation sexual reproduction reproductive process multicellular organismal reproductive process male germ cell proliferation gamete generation cellular response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction regulation of response to stimulus MAPK cascade regulation of cell communication negative regulation of MAPK cascade axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization axon target recognition nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development cellular response to chemical stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus protein deubiquitination protein modification by small protein removal macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation or removal adult walking behavior adult locomotory behavior adult behavior locomotory behavior walking behavior muscle structure development muscle cell development muscle cell differentiation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cell projection neuron projection terminus neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body neuronal cell body neuron projection cytoplasm axon axon cytoplasm cytoplasmic region plasma membrane bounded cell projection cytoplasm
A [auth C], B [auth D]	Polyubiquitin-C	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR001578	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	Domain
C [auth A], D [auth B]	IPR057254	Ubiquitin carboxyl-terminal hydrolase family 1, cysteine active-site	Conserved Site
C [auth A], D [auth B]	IPR036959	Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily	Homologous Superfamily
A [auth C], B [auth D]	IPR019954	Ubiquitin conserved site	Conserved Site
A [auth C], B [auth D]	IPR000626	Ubiquitin-like domain	Domain
A [auth C], B [auth D]	IPR019956	Ubiquitin domain	Domain
A [auth C], B [auth D]	IPR050158	Ubiquitin and ubiquitin-like	Family
A [auth C], B [auth D]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A], D [auth B]	Pharos: P09936	early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome non-small cell lung carcinoma Parkinson disease 5, autosomal dominant, susceptibility to Parkinson disease hereditary spastic paraplegia gallbladder cancer peripheral nervous system disease neurodegenerative disease peripheral neuropathy esophageal cancer lung adenocarcinoma malignant colon neoplasm medulloblastoma acute myeloid leukemia Ataxias, Hereditary early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome non-small cell lung carcinoma Parkinson disease 5, autosomal dominant, susceptibility to Parkinson disease hereditary spastic paraplegia gallbladder cancer peripheral nervous system disease neurodegenerative disease peripheral neuropathy esophageal cancer lung adenocarcinoma malignant colon neoplasm medulloblastoma acute myeloid leukemia Ataxias, Hereditary ovarian cancer breast cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cystic fibrosis Pick disease head and neck cancer large cell medulloblastoma lung cancer malignant ependymoma neoplasm of esophagus adenoma oligodendroglioma atopic eczema pancreatic intraductal papillary-mucinous carcinoma chronic obstructive pulmonary disease paraplegia diabetes mellitus Emery-Dreifuss muscular dystrophy pilocytic astrocytoma gallbladder neoplasm hepatocellular carcinoma lung carcinoma malignant glioma astrocytic tumor osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm congenital diaphragmatic hernia psoriasis glioblastoma
A [auth C], B [auth D]	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer

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.