4NNJ

Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4nnjb1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d4nnjb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
E	d4nnje1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
E	d4nnje2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d4nnjd1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d4nnjd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

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	8003540	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003540	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003552	3000140	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SCCH domain-like	8003543	3000139	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FCCH domain-like	8003532	3000138	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	E2 binding domain-like	8003942	3000147	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003540	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E2 binding domain-like	8003942	3000147	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FCCH domain-like	8003532	3000138	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003540	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003552	3000140	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SCCH domain-like	8003543	3000139	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8040187	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8040187	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8040187	3000157	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	E1_FCCH	e4nnjA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: E1_FCCH	ECOD (1.6)
A	UBA_e1_thiolCys	e4nnjA4	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)
A	ThiF_3	e4nnjA2	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: ThiF_3	ECOD (1.6)
A	E1_UFD	e4nnjA1	A: a+b two layers	X: beta-Grasp	H: E2-binding domain of E1 (From Topology)	T: E2-binding domain of E1	F: E1_UFD	ECOD (1.6)
A	ThiF_1	e4nnjA6	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	ThiF_3	e4nnjA5	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	E1_FCCH	e4nnjC3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: E1_FCCH	ECOD (1.6)
C	UBA_e1_thiolCys	e4nnjC1	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)
C	ThiF_3	e4nnjC6	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: ThiF_3	ECOD (1.6)
C	E1_UFD	e4nnjC4	A: a+b two layers	X: beta-Grasp	H: E2-binding domain of E1 (From Topology)	T: E2-binding domain of E1	F: E1_UFD	ECOD (1.6)
C	ThiF_1	e4nnjC7	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)
C	ThiF_3	e4nnjC5	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)
B	ubiquitin_1	e4nnjB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
E	ubiquitin_1	e4nnjE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D	ubiquitin_1	e4nnjD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.50.50.80	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1	CATH (4.3.0)
A	3.40.50.12550	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2	CATH (4.3.0)
A	2.40.30.180	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	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)
A	1.10.10.2660	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ubiquitin-activating enzyme E1, SCCH domain	CATH (4.3.0)
A	3.10.290.60	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
C	3.50.50.80	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1	CATH (4.3.0)
C	3.40.50.12550	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2	CATH (4.3.0)
C	2.40.30.180	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	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)
C	1.10.10.2660	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ubiquitin-activating enzyme E1, SCCH domain	CATH (4.3.0)
C	3.10.290.60	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
A, C	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, C	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, C	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, C	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, D, E	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
A, C	Ubiquitin-activating enzyme E1 1	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 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	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 protein metabolic process macromolecule 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	intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B, D, E	Uba1	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme 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 protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein 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 protein metabolic process macromolecule 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle peroxisome microbody

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR042302	Ubiquitin-activating enzyme E1, FCCH domain superfamily	Homologous Superfamily
A, C	IPR000011	Ubiquitin/SUMO-activating enzyme E1-like	Family
A, C	IPR045886	ThiF/MoeB/HesA family	Family
A, C	IPR042449	Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1	Homologous Superfamily
A, C	IPR019572	Ubiquitin-activating enzyme, SCCH domain	Domain
A, C	IPR042063	Ubiquitin-activating enzyme E1, SCCH domain	Homologous Superfamily
A, C	IPR000594	THIF-type NAD/FAD binding fold	Domain
A, C	IPR032420	Ubiquitin-activating enzyme E1, four-helix bundle	Domain
A, C	IPR018075	Ubiquitin-activating enzyme E1	Family
A, C	IPR032418	Ubiquitin-activating enzyme E1, FCCH domain	Domain
A, C	IPR018965	Ubiquitin-activating enzyme E1, C-terminal	Domain
A, C	IPR035985	Ubiquitin-activating enzyme	Homologous Superfamily
A, C	IPR033127	Ubiquitin-activating enzyme E1, Cys active site	Active Site
A, C	IPR038252	Ubiquitin-activating enzyme E1, C-terminal domain superfamily	Homologous Superfamily
A, C	IPR018074	Ubiquitin-activating enzyme E1, conserved site	Conserved Site
B, D, E	IPR019956	Ubiquitin domain	Domain
B, D, E	IPR019954	Ubiquitin conserved site	Conserved Site
B, D, E	IPR050158	Ubiquitin and ubiquitin-like	Family
B, D, E	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D, E	IPR000626	Ubiquitin-like domain	Domain

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4NNJ

Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage