1YOV

Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8

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)
B	d1yovb_	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)
D	d1yovd_	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)
A	d1yova_	Alpha and beta proteins (a/b)	Activating enzymes of the ubiquitin-like proteins	Activating enzymes of the ubiquitin-like proteins	Ubiquitin activating enzymes (UBA)	Amyloid beta precursor protein-binding protein 1, APPBP1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1yovc_	Alpha and beta proteins (a/b)	Activating enzymes of the ubiquitin-like proteins	Activating enzymes of the ubiquitin-like proteins	Ubiquitin activating enzymes (UBA)	Amyloid beta precursor protein-binding protein 1, APPBP1	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)
B	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003542	3000112	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003549	3000140	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003542	3000112	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003542	3000112	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003542	3000112	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003549	3000140	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003537	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003537	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003548	3000140	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Duplicated CC (catalytic cysteine) domain-like	8003546	3000141	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Duplicated CC (catalytic cysteine) domain-like	8003546	3000141	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003548	3000140	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003537	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003537	3000112	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)
B	UBA_e1_thiolCys	e1yovB3	A: alpha arrays	X: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	H: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	T: Catalytic cysteine domain in ubiquitin-activating enzyme	F: UBA_e1_thiolCys	ECOD (1.6)
B	E2_bind	e1yovB1	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)
B	ThiF_1	e1yovB4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_1	ECOD (1.6)
D	UBA_e1_thiolCys	e1yovD3	A: alpha arrays	X: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	H: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	T: Catalytic cysteine domain in ubiquitin-activating enzyme	F: UBA_e1_thiolCys	ECOD (1.6)
D	E2_bind	e1yovD4	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)
D	ThiF_1	e1yovD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_1	ECOD (1.6)
A	APPBP1_RUB	e1yovA2	A: alpha arrays	X: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	H: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	T: Catalytic cysteine domain in ubiquitin-activating enzyme	F: APPBP1_RUB	ECOD (1.6)
A	ThiF_3	e1yovA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_3	ECOD (1.6)
C	ThiF_2,APPBP1_RUB	e1yovC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_2,APPBP1_RUB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.10.10.520	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ubiquitin activating enzymes (Uba3). Chain: B, domain 2	CATH (4.3.0)
B	3.10.20.260	Alpha Beta	Roll	Ubiquitin-like (UB roll)	NEDD8-activating enzyme E1, catalytic subunit	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	1.10.10.520	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ubiquitin activating enzymes (Uba3). Chain: B, domain 2	CATH (4.3.0)
D	3.10.20.260	Alpha Beta	Roll	Ubiquitin-like (UB roll)	NEDD8-activating enzyme E1, catalytic subunit	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
B, D	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
A, C	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	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	macromolecule modification metabolic process cellular 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 macromolecule modification metabolic process cellular 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 cell cycle regulation of cell cycle endomitotic cell cycle mitotic cell cycle proteolysis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
A, C	Amyloid protein-binding protein 1	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 protein heterodimerization activity protein binding binding protein dimerization activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme 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 protein heterodimerization activity protein binding binding protein dimerization activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding NEDD8 activating enzyme activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of cell cycle phase transition signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of cell cycle phase transition signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle DNA replication checkpoint signaling regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process mitotic DNA replication checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition 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 protein metabolic process macromolecule metabolic process multicellular organismal process regulation of cellular component organization cellular component organization cellular component biogenesis multicellular organism development cellular component assembly regulation of postsynapse assembly cell junction assembly anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development developmental process postsynapse organization postsynapse assembly regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly neuron apoptotic process apoptotic process cell death programmed cell death regulation of apoptotic process regulation of programmed cell death regulation of neuron apoptotic process macromolecule modification post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal protein ubiquitination	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex synapse cell junction glutamatergic synapse membrane-bounded organelle intracellular organelle organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex synapse cell junction glutamatergic synapse membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR030468	NEDD8-activating enzyme E1 catalytic subunit, N-terminal domain	Domain
B, D	IPR014929	E2 binding	Domain
B, D	IPR045886	ThiF/MoeB/HesA family	Family
B, D	IPR000594	THIF-type NAD/FAD binding fold	Domain
B, D	IPR035985	Ubiquitin-activating enzyme	Homologous Superfamily
B, D	IPR033127	Ubiquitin-activating enzyme E1, Cys active site	Active Site
B, D	IPR023318	Ubiquitin activating enzyme, alpha domain superfamily	Homologous Superfamily
A, C	IPR045886	ThiF/MoeB/HesA family	Family
A, C	IPR030667	NEDD8-activating enzyme E1 regulatory subunit APP-BP1	Family
A, C	IPR000594	THIF-type NAD/FAD binding fold	Domain
A, C	IPR035985	Ubiquitin-activating enzyme	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q8TBC4	amyotrophic lateral sclerosis lymphoplasmacytic lymphoma dermatomyositis myopathy juvenile dermatomyositis plasma cell myeloma
A, C	Pharos: Q13564	lung cancer pancreatic intraductal papillary-mucinous neoplasm medulloblastoma plasma cell myeloma 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.