3CMM
Crystal Structure of the Uba1-Ubiquitin Complex
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
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) |
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) |
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) |
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) |
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 | 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) |
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) |
D | ubiquitin_1 | e3cmmD1 | 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
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] | 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] | 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 ... | 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 ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
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] | EC: 6.3.2.19 (PDB Primary Data) EC: 6.2.1.45 (UniProt) | |
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] | EC: 6.3.2.19 (PDB Primary Data) EC: 6.2.1.45 (UniProt) |