2O25 | pdb_00002o25

Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d2o25c_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2o25d_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2o25a1	All alpha proteins	RuvA C-terminal domain-like	UBA-like	UBA domain	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2o25a2	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin-conjugating enzyme E2-25 kDa, E2 domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2o25b1	All alpha proteins	RuvA C-terminal domain-like	UBA-like	UBA domain	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2o25b2	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin-conjugating enzyme E2-25 kDa, E2 domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	UBC-like	8041006	3000570	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UBA-like	8041004	3001235	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	UBA-like	8041004	3001235	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	UBC-like	8041006	3000570	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	RWD	e2o25C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RWD	ECOD (v294.1)
D	RWD	e2o25D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RWD	ECOD (v294.1)
A	UBA	e2o25A1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: UBA	ECOD (v294.1)
A	RWD	e2o25A2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RWD	ECOD (v294.1)
B	UBA	e2o25B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: UBA	ECOD (v294.1)
B	RWD	e2o25B2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RWD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
D	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
A	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
B	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	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
A, B	PF00627	UBA/TS-N domain (UBA)	UBA/TS-N domain	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin a ...	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle [1]. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU [2]. The domain has been found in non EF-TS proteins such as alpha-NAC Swiss:P70670 and MJ0280 Swiss:Q57728 [1].	Domain
A, B	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
C, D	SUMO-1-conjugating enzyme UBC9	protein binding binding small protein activating enzyme binding enzyme binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO conjugating enzyme activity SUMO transferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity RING-like zinc finger domain binding protein binding binding small protein activating enzyme binding enzyme binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO conjugating enzyme activity SUMO transferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity RING-like zinc finger domain binding protein domain specific binding RNA binding nucleic acid binding transcription factor binding transcription coregulator 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 HLH domain binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling macromolecule modification protein metabolic process protein modification process cell division cell cycle chromosome segregation cell cycle process peptidyl-lysine modification protein sumoylation peptidyl-amino acid modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal mitotic nuclear membrane reassembly membrane biogenesis mitotic cell cycle nuclear membrane reassembly cellular component organization cellular component biogenesis cellular component assembly cellular component organization or biogenesis endomembrane system organization membrane organization mitotic nuclear division organelle fission nuclear membrane organization membrane assembly nuclear division organelle organization nucleus organization mitotic cell cycle process mitotic nuclear membrane organization nuclear envelope organization catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process trans-synaptic signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport nuclear export establishment of localization positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	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 presynapse presynaptic cytosol 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 presynapse presynaptic cytosol synapse cell junction protein-containing complex nuclear protein-containing complex nuclear pore membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen glutamatergic synapse catalytic complex SUMO ligase complex transferase complex condensed nuclear chromosome intracellular membraneless organelle nuclear chromosome chromosome membraneless organelle synaptonemal structure synaptonemal complex condensed chromosome Schaffer collateral - CA1 synapse perinuclear region of cytoplasm nuclear body PML body postsynapse postsynaptic cytosol
A, B	Ubiquitin-conjugating enzyme E2-25 kDa	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 aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus positive regulation of cell communication regulation of cellular process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway biological regulation response to peptide regulation of response to cytokine stimulus regulation of response to stimulus response to chemical regulation of cell communication response to tumor necrosis factor positive regulation of cytokine-mediated signaling pathway positive regulation of signaling 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 protein K48-linked ubiquitination proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process regulation of protein metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of proteasomal protein catabolic process regulation of metabolic process regulation of protein catabolic process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-threonine phosphorylation positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process peptidyl-threonine modification positive regulation of protein phosphorylation phosphorus metabolic process protein phosphorylation positive regulation of phosphorus metabolic process positive regulation of peptidyl-threonine phosphorylation phosphorylation regulation of phosphorus metabolic process regulation of phosphorylation peptidyl-threonine phosphorylation protein polymerization protein-containing complex organization homeostatic process free ubiquitin chain polymerization cellular component organization cellular component biogenesis cellular component assembly cellular homeostasis protein-containing complex assembly cellular component organization or biogenesis ubiquitin recycling positive regulation of response to biotic stimulus regulation of type I interferon-mediated signaling pathway response to biotic stimulus interferon-mediated signaling pathway cellular response to type I interferon positive regulation of immune response regulation of immune system process positive regulation of immune system process immune response response to other organism regulation of innate immune response response to external stimulus defense response to other organism positive regulation of defense response regulation of immune response response to type I interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of type I interferon-mediated signaling pathway positive regulation of response to external stimulus regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of innate immune response defense response defense response to symbiont immune system process type I interferon-mediated signaling pathway cellular response to interferon-beta response to interferon-beta	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol filopodium tip cell projection actin-based cell projection filopodium plasma membrane bounded cell projection membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
C, D	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
C, D	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
C, D	IPR050113	Ubiquitin-conjugating enzyme E2-like	Family
A, B	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A, B	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A, B	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
A, B	IPR009060	UBA-like superfamily	Homologous Superfamily
A, B	IPR042599	Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain	Domain
A, B	IPR015940	Ubiquitin-associated domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P63279	sarcomatoid carcinoma carcinoma Mammary Neoplasms, Experimental psoriasis undifferentiated carcinoma breast cancer glioblastoma lung cancer mammary neoplasms, animal non-small cell lung carcinoma pituitary cancer invasive ductal breast carcinoma lymphoplasmacytic lymphoma osteosarcoma plasma cell myeloma sarcomatoid carcinoma carcinoma Mammary Neoplasms, Experimental psoriasis undifferentiated carcinoma breast cancer glioblastoma lung cancer mammary neoplasms, animal non-small cell lung carcinoma pituitary cancer invasive ductal breast carcinoma lymphoplasmacytic lymphoma osteosarcoma plasma cell myeloma tuberculosis atypical teratoid rhabdoid tumor large cell medulloblastoma medulloblastoma ovarian cancer
A, B	Pharos: P61086	astrocytic tumor lung cancer myopathy subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor malignant ependymoma ovarian cancer glioblastoma malignant glioma plasma cell myeloma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.