3CMM

Crystal Structure of the Uba1-Ubiquitin Complex

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3cmmd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C [auth B]	d3cmmb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	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	SCCH domain-like	8003543	3000139	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FCCH domain-like	8003532	3000138	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003552	3000140	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)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003540	3000112	SCOP2B (2022-06-29)
B [auth C]	SCOP2 Family	Ubiquitin activating enzymes UBA2-like	8003511	4000345	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Family	Ubiquitin activating enzymes SAE1-like	8003525	4000139	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Family	FCCH domain of UBA1	8003531	4000349	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Family	E2 binding domain-like	8052336	4004110	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	SCCH domain-like	8003543	3000139	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	FCCH domain-like	8003532	3000138	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	E2 binding domain-like	8003942	3000147	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	Activating enzymes of the ubiquitin-like proteins	8003540	3000112	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	CC (catalytic cysteine) domain-like	8003552	3000140	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8040187	3000157	SCOP2B (2022-06-29)
C [auth B]	SCOP2 Family	Ubiquitin-related	8027808	4000962	SCOP2 (2022-06-29)
C [auth B]	SCOP2 Superfamily	Ubiquitin-like	8040187	3000157	SCOP2 (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	e3cmmA4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: E1_FCCH	ECOD (1.6)
A	UBA_e1_thiolCys	e3cmmA6	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	e3cmmA5	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	e3cmmA3	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	e3cmmA2	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	e3cmmA1	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 [auth C]	E1_FCCH	e3cmmC2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: E1_FCCH	ECOD (1.6)
B [auth C]	UBA_e1_thiolCys	e3cmmC4	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 [auth C]	ThiF_3	e3cmmC6	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)
B [auth C]	E1_UFD	e3cmmC1	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)
B [auth C]	ThiF_1	e3cmmC3	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)
B [auth C]	ThiF_3	e3cmmC5	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)
D	ubiquitin_1	e3cmmD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
C [auth B]	ubiquitin_1	e3cmmB1	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)
B [auth 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)
B [auth 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)
B [auth C]	2.40.30.180	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B [auth C]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B [auth C]	1.10.10.2660	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ubiquitin-activating enzyme E1, SCCH domain	CATH (4.3.0)
B [auth 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)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C [auth B]	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, B [auth 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, B [auth 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, B [auth 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, B [auth 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, B [auth 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
C [auth B], D	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, B [auth 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 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-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 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 membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
C [auth B], D	Ubiquitin	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 cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule 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 cellular 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 peroxisome microbody

InterPro: Protein Family Classification InterPro Database Homepage

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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	E1 ubiquitin-activating enzyme M-CSA #307	Ubiquitination is mediated by three enzymes, E1 (PDB:3cmm), E2 (PDB:1ayz) and E3 (PDB:1c4z). The first, E1, is essential for ubiquitin activation and transferring the substrate onto the second cascade enzyme, E2, which responsible for mediating repeated ubiquitination at the eventual substrate, which is brought into proximity of E2 by the active site of E3, the enzyme which also regulates substrate specificity. This cascade regulates the ubiquitination of specific proteins, generating post-translational modifications that activate a number of possible cellular responses, depending upon the site and type of ubiquitin marker. This entry represents the first of the three reactions occurring in this cascade: ubiquitin:[E1 ubiquitin-activating enzyme] ligase (AMP-forming). E1 catalyses the ATP-dependent activation of ubiquitin through the formation of a thioester bond between the C-terminal glycine of ubiquitin and the sulfhydryl side group of a cysteine residue in the E1 protein. Several E1 type enzymes have been identified to catalyse substrate-specific transfer reactions for ubiquitin-like proteins, although a number of these enzymes will also catalyse the transfer of ubiquitin and other ubiquitin-like proteins.	Defined by 8 residues: ARG:A-12 [auth A-21]ARG:A-472 [auth A-481]ASP:A-535 [auth A-544]CYS:A-591 [auth A-600]THR:A-592 [auth A-601]ARG:A-594 [auth A-603]ASN:A-772 [auth A-781]ASP:A-773 [auth A-782] \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 6.3.2.19 (PDB Primary Data) EC: 6.2.1.45 (UniProt)
A	E2 ubiquitin-conjugating enzyme M-CSA #939	Ubiquitination is mediated by three enzymes, E1 (PDB:3cmm), E2 (PDB:1ayz) and E3 (PDB:1c4z). The first, E1, is essential for ubiquitin activation and transferring the substrate onto the second cascade enzyme, E2, which responsible for mediating repeated ubiquitination at the eventual substrate, which is brought into proximity of E2 by the active site of E3, the enzyme which also regulates substrate specificity. This entry represents the second of the three reactions occurring in this cascade: ubiquitin:[E1 ubiquitin-activating enzyme] ligase (AMP-forming). The E2 ubiquitin-conjugating enzyme acquires the activated ubquitin from the E1 ubiquitin-activating enzyme (EC 6.2.1.45) and binds it via a transthioesterification reaction to itself. In the human enzyme the catalytic centre is located at Cys-87 where ubiquitin is bound via its C-terminal glycine in a thioester linkage.	Defined by 5 residues: CYS:A-591 [auth A-600]THR:A-592 [auth A-601]ARG:A-594 [auth A-603]ASN:A-772 [auth A-781]ASP:A-773 [auth A-782] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.3.2.19 (PDB Primary Data) Search M-CSA Motif + EC 6.3.2.19 EC: 6.2.1.45 (UniProt) Search M-CSA Motif + EC 6.2.1.45