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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyActivating enzymes of the ubiquitin-like proteins 8003540 3000112 SCOP2B (2022-06-29)
ASCOP2B SuperfamilySCCH domain-like 8003543 3000139 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyActivating enzymes of the ubiquitin-like proteins 8017546 3000112 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyFCCH domain-like 8003532 3000138 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCC (catalytic cysteine) domain-like 8003552 3000140 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyE2 binding domain-like 8003942 3000147 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyActivating enzymes of the ubiquitin-like proteins 8017546 3000112 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyActivating enzymes of the ubiquitin-like proteins 8003540 3000112 SCOP2B (2022-06-29)
B [auth C]SCOP2 FamilyUbiquitin activating enzymes UBA2-like 8003511 4000345 SCOP2 (2022-06-29)
B [auth C]SCOP2 FamilyUbiquitin activating enzymes SAE1-like 8003525 4000139 SCOP2 (2022-06-29)
B [auth C]SCOP2 FamilyFCCH domain of UBA1 8003531 4000349 SCOP2 (2022-06-29)
B [auth C]SCOP2 FamilyE2 binding domain-like 8052336 4004110 SCOP2 (2022-06-29)
B [auth C]SCOP2 SuperfamilySCCH domain-like 8003543 3000139 SCOP2 (2022-06-29)
B [auth C]SCOP2 SuperfamilyActivating enzymes of the ubiquitin-like proteins 8017546 3000112 SCOP2 (2022-06-29)
B [auth C]SCOP2 SuperfamilyFCCH domain-like 8003532 3000138 SCOP2 (2022-06-29)
B [auth C]SCOP2 SuperfamilyE2 binding domain-like 8003942 3000147 SCOP2 (2022-06-29)
B [auth C]SCOP2 SuperfamilyActivating enzymes of the ubiquitin-like proteins 8003540 3000112 SCOP2 (2022-06-29)
B [auth C]SCOP2 SuperfamilyCC (catalytic cysteine) domain-like 8003552 3000140 SCOP2 (2022-06-29)
C [auth B]SCOP2 FamilyUbiquitin-related 8027808 4000962 SCOP2 (2022-06-29)
C [auth B]SCOP2 SuperfamilyUbiquitin-like 8040187 3000157 SCOP2 (2022-06-29)
DSCOP2B SuperfamilyUbiquitin-like 8040187 3000157 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AE1_FCCHe3cmmA4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: E1_FCCHECOD (1.6)
AUBA_e1_thiolCyse3cmmA6 A: alpha arraysX: 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 enzymeF: UBA_e1_thiolCysECOD (1.6)
AThiF_3e3cmmA5 A: alpha arraysX: 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 enzymeF: ThiF_3ECOD (1.6)
AE1_UFDe3cmmA3 A: a+b two layersX: beta-GraspH: E2-binding domain of E1 (From Topology)T: E2-binding domain of E1F: E1_UFDECOD (1.6)
AThiF_1e3cmmA2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: Activating enzymes of the ubiquitin-like proteinsF: ThiF_1ECOD (1.6)
AThiF_3e3cmmA1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: Activating enzymes of the ubiquitin-like proteinsF: ThiF_3ECOD (1.6)
B [auth C]E1_FCCHe3cmmC2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: E1_FCCHECOD (1.6)
B [auth C]UBA_e1_thiolCyse3cmmC4 A: alpha arraysX: 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 enzymeF: UBA_e1_thiolCysECOD (1.6)
B [auth C]ThiF_3e3cmmC6 A: alpha arraysX: 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 enzymeF: ThiF_3ECOD (1.6)
B [auth C]E1_UFDe3cmmC1 A: a+b two layersX: beta-GraspH: E2-binding domain of E1 (From Topology)T: E2-binding domain of E1F: E1_UFDECOD (1.6)
B [auth C]ThiF_1e3cmmC3 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: Activating enzymes of the ubiquitin-like proteinsF: ThiF_1ECOD (1.6)
B [auth C]ThiF_3e3cmmC5 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: Activating enzymes of the ubiquitin-like proteinsF: ThiF_3ECOD (1.6)
C [auth B]ubiquitin_1e3cmmB1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_1ECOD (1.6)
Dubiquitin_1e3cmmD1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.50.50.80 Alpha Beta 3-Layer(bba) Sandwich FAD/NAD(P)-binding domain Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1CATH (4.3.0)
A3.40.50.12550 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2CATH (4.3.0)
A2.40.30.180 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (4.3.0)
A3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
A1.10.10.2660 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Ubiquitin-activating enzyme E1, SCCH domainCATH (4.3.0)
A3.10.290.60 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region Chain ACATH (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 1CATH (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 2CATH (4.3.0)
B [auth C]2.40.30.180 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (4.3.0)
B [auth C]3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
B [auth C]1.10.10.2660 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Ubiquitin-activating enzyme E1, SCCH domainCATH (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 ACATH (4.3.0)
C [auth B]3.10.20.90 Alpha Beta Roll Ubiquitin-like (UB roll) Phosphatidylinositol 3-kinase Catalytic SubunitCATH (4.3.0)
D3.10.20.90 Alpha Beta Roll Ubiquitin-like (UB roll) Phosphatidylinositol 3-kinase Catalytic SubunitCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A,
B [auth C]
PF00899ThiF family (ThiF)ThiF familyThis 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]
PF09358Ubiquitin fold domain (E1_UFD)Ubiquitin fold domainThe 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]
PF10585Ubiquitin-activating enzyme, SCCH domain (UBA_E1_SCCH)Ubiquitin-activating enzyme, SCCH domainUbiquitin-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]
PF16190Ubiquitin-activating enzyme E1 FCCH domain (E1_FCCH)Ubiquitin-activating enzyme E1 FCCH domainThis domain is found in the ubiquitin-activating E1 family enzymes [1].Domain
A,
B [auth C]
PF16191Ubiquitin-activating enzyme E1 four-helix bundle (E1_4HB)Ubiquitin-activating enzyme E1 four-helix bundleThis domain is found in the ubiquitin-activating E1 family enzymes [1].Domain
C [auth B],
D
PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A,
B [auth C]
Ubiquitin-activating enzyme E1 1
C [auth B],
D
Ubiquitin

InterPro: Protein Family Classification InterPro Database Homepage

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

ChainsEnzyme NameDescriptionCatalytic 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]
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Explore in 3DM-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)
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]
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Explore in 3DM-CSA Motif Definition