9B5P | pdb_00009b5p

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 1 map and model (ATP/Mg)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8052356	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	E2 binding domain-like	8052338	3000147	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8052351	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8052354	3000140	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SCCH domain-like	8052355	3000139	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FCCH domain-like	8052344	3000138	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	UBC-like	8059966	3000570	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00899	ThiF family (ThiF)	ThiF family	This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1 [1-3].	Domain
A	PF09358	Ubiquitin fold domain (E1_UFD)	Ubiquitin fold domain	The ubiquitin fold domain is found at the C-terminus of ubiquitin-activating E1 family enzymes. This domain binds to E2 enzymes [1].	Domain
A	PF10585	Ubiquitin-activating enzyme, SCCH domain (UBA_E1_SCCH)	Ubiquitin-activating enzyme, SCCH domain	Ubiquitin-activating enzyme (E1 enzyme) activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free A ...	Ubiquitin-activating enzyme (E1 enzyme) activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin-conjugating enzymes (E2) [1]. This domain carries the last of five conserved cysteines that is part of the active site of the enzyme, responsible for ubiquitin thiolester complex formation, the active site being represented by the sequence motif PICTLKNFP [2,3,4]. The catalytic cysteine domain contains the E1 active site cysteine, and is divided in two half-domains, FCCH and SCCH, for 'first' and 'second' catalytic cysteine half-domain, respectively. This is the SCCH domain in which resides the catalytic cysteine [5].	Domain
A	PF16190	Ubiquitin-activating enzyme E1 FCCH domain (E1_FCCH)	Ubiquitin-activating enzyme E1 FCCH domain	This domain is found in the ubiquitin-activating E1 family enzymes [1].	Domain
A	PF16191	Ubiquitin-activating enzyme E1 four-helix bundle (E1_4HB)	Ubiquitin-activating enzyme E1 four-helix bundle	This domain is found in the ubiquitin-activating E1 family enzymes [1].	Domain
B [auth C]	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin-activating enzyme E1 1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ubiquitin-like modifier activating enzyme activity ligase activity, forming carbon-sulfur bonds catalytic activity, acting on a protein ubiquitin activating enzyme activity catalytic activity ligase activity ATP-dependent activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process 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 cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process 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 ubiquitin-dependent protein catabolic process metabolic 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B [auth C]	Ubiquitin-conjugating enzyme E2 4	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 ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity	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 ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process protein polyubiquitination 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 ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process protein polyubiquitination 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 positive regulation of organelle organization regulation of cell cycle phase transition regulation of cellular process regulation of mitotic nuclear division positive regulation of mitotic nuclear division positive regulation of mitotic metaphase/anaphase transition positive regulation of mitotic cell cycle phase transition cell cycle mitotic sister chromatid separation chromosome segregation regulation of biological process regulation of cell cycle process positive regulation of nuclear division sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition mitotic cell cycle process regulation of chromosome separation regulation of chromosome segregation regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization regulation of mitotic sister chromatid separation positive regulation of cellular component organization positive regulation of biological process cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle positive regulation of metaphase/anaphase transition of cell cycle mitotic sister chromatid segregation positive regulation of cell cycle process positive regulation of mitotic cell cycle cellular component organization or biogenesis regulation of cell cycle positive regulation of cellular process cell cycle process mitotic nuclear division organelle fission biological regulation chromosome organization positive regulation of cell cycle organelle organization nuclear division chromosome separation regulation of sister chromatid segregation positive regulation of cell cycle phase transition positive regulation of mitotic sister chromatid separation regulation of nuclear division nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle positive regulation of chromosome separation metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition cellular response to stimulus response to stimulus cellular response to sterol depletion signaling response to sterol depletion intracellular signal transduction cell communication SREBP signaling pathway cellular response to stress response to stress ER-nucleus signaling pathway signal transduction proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
C [auth D]	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding structural molecule activity structural constituent of ribosome	biosynthetic process cytoplasmic translation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis biosynthetic process cytoplasmic translation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis 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 nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol protein-containing complex ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome ribonucleoprotein complex ribosome large ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR042302	Ubiquitin-activating enzyme E1, FCCH domain superfamily	Homologous Superfamily
A	IPR000011	Ubiquitin/SUMO-activating enzyme E1-like	Family
A	IPR045886	ThiF/MoeB/HesA family	Family
A	IPR042449	Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1	Homologous Superfamily
A	IPR019572	Ubiquitin-activating enzyme, SCCH domain	Domain
A	IPR042063	Ubiquitin-activating enzyme E1, SCCH domain	Homologous Superfamily
A	IPR000594	THIF-type NAD/FAD binding fold	Domain
A	IPR032420	Ubiquitin-activating enzyme E1, four-helix bundle	Domain
A	IPR018075	Ubiquitin-activating enzyme E1	Family
A	IPR032418	Ubiquitin-activating enzyme E1, FCCH domain	Domain
A	IPR018965	Ubiquitin-activating enzyme E1, C-terminal	Domain
A	IPR035985	Ubiquitin-activating enzyme	Homologous Superfamily
A	IPR033127	Ubiquitin-activating enzyme E1, Cys active site	Active Site
A	IPR038252	Ubiquitin-activating enzyme E1, C-terminal domain superfamily	Homologous Superfamily
B [auth C]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B [auth C]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
B [auth C]	IPR000608	Ubiquitin-conjugating enzyme E2, catalytic core domain	Domain
C [auth D]	IPR019954	Ubiquitin conserved site	Conserved Site
C [auth D]	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
C [auth D]	IPR000626	Ubiquitin-like domain	Domain
C [auth D]	IPR019956	Ubiquitin domain	Domain
C [auth D]	IPR050158	Ubiquitin and ubiquitin-like	Family
C [auth D]	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
C [auth D]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily