1Y8X

Structural basis for recruitment of Ubc12 by an E2-binding domain in NEDD8's E1

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1y8xa1	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	d1y8xa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1y8xb1	Alpha and beta proteins (a/b)	Activating enzymes of the ubiquitin-like proteins	Activating enzymes of the ubiquitin-like proteins	Ubiquitin activating enzymes (UBA)	UBA3	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	SCOP2 Family	UBC-related	8021839	4001046	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	UBC-like	8034219	3000570	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	E2 binding domain-like	8003941	3000147	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)
A	UQ_con	e1y8xA1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
B	E2_bind	e1y8xB1	A: a+b two layers	X: beta-Grasp	H: E2-binding domain of E1 (From Topology)	T: E2-binding domain of E1	F: E2_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
B	3.10.290.20	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B	PF08825	E2 binding domain (E2_bind)	E2 binding domain	E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The domain resembles ubiquitin, and recruits the catalytic core of the E2 enz ...	E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The domain resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin-conjugating enzyme E2 M	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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 NEDD8 transferase activity catalytic activity, acting on a protein acyltransferase activity NEDD8 conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity	organic substance metabolic process organonitrogen compound metabolic process macromolecule modification nitrogen compound metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process regulation of biological process neuron apoptotic process positive regulation of programmed cell death regulation of cellular process organic substance metabolic process organonitrogen compound metabolic process macromolecule modification nitrogen compound metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process regulation of biological process neuron apoptotic process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process cellular process apoptotic process positive regulation of neuron apoptotic process programmed cell death positive regulation of cellular process regulation of neuron apoptotic process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B	Ubiquitin-activating enzyme E1C	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein heterodimerization activity protein binding protein dimerization activity aminoacyltransferase activity ubiquitin-like protein transferase activity NEDD8 transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity NEDD8 activating enzyme activity ubiquitin-like modifier activating enzyme activity ligase activity, forming carbon-sulfur bonds ligase activity ATP-dependent activity identical protein binding	organic substance metabolic process organonitrogen compound metabolic process macromolecule modification nitrogen compound metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of biological process organic substance metabolic process organonitrogen compound metabolic process macromolecule modification nitrogen compound metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of biological process regulation of cellular process biological regulation cellular process cell cycle regulation of cell cycle endomitotic cell cycle mitotic cell cycle proteolysis	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
A	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
B	IPR030468	NEDD8-activating enzyme E1 catalytic subunit, N-terminal domain	Domain
B	IPR014929	E2 binding	Domain
B	IPR045886	ThiF/MoeB/HesA family	Family
B	IPR000594	THIF-type NAD/FAD binding fold	Domain
B	IPR035985	Ubiquitin-activating enzyme	Homologous Superfamily
B	IPR033127	Ubiquitin-activating enzyme E1, Cys active site	Active Site
B	IPR023318	Ubiquitin activating enzyme, alpha domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P61081	astrocytic tumor dermatomyositis oligodendroglioma psoriasis colorectal adenoma glioblastoma osteosarcoma colorectal cancer lung cancer plasma cell myeloma
B	Pharos: Q8TBC4	amyotrophic lateral sclerosis lymphoplasmacytic lymphoma dermatomyositis myopathy juvenile dermatomyositis plasma cell myeloma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.