Overview for MACiE Entry M0307

Version history

General Information

EC Number: (A member of the Ligases, Forming carbon-nitrogen bonds, Acid—amino-acid ligases (peptide synthases))

Enzyme Name: Ubiquitin transfer cascade (E1, E2, E3)

Biological Species: Saccharomyces cerevisiae (Baker's Yeast)

Catalytic Chain UniprotKB Accession Codes:

    Representative PDB Code: 3cmm - CRYSTAL STRUCTURE OF THE UBA1-UBIQUITIN COMPLEX (Resolution = 2.70 Å).

    Catalytic CATH Codes:

    • Unassigned Domain

    "Other" CATH Codes:

    • - Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

    Display structure information

    Overall Reaction:

    Image of ATP

    Image of Protein lysine

    Image of ubiquitin

    right arrow

    Image of adenylated ubiquitin

    Image of Ubiqutinated protein lysine

    Image of diphosphate

    Image of AMP

    2 ATP
    Protein lysine
    2 ubiquitin
    adenylated ubiquitin
    Ubiqutinated protein lysine
    2 diphosphate

    Overall Comment: 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. 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.

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    Stepwise Description of the Reaction

    Step 1The C terminus of ubiquitin attacks the alpha phosphate of ATP within the adenylation binding site.
    Step 2An unidentified base activates Cys600A towards nucleophilic attack at the adenylated ubiquitin.
    Step 3The tetrahedral anionic intermediate collapses, releasing AMP and forming the enzyme-substrate adduct.
    Step 4The C terminus of ubiquitin attacks the alpha phosphate of ATP within the adenylation binding site.
    Step 5The ubiquitin accepting enzyme E2 attacks the high energy thioester bond at the active site of E1, forming an oxyanion intermediate.
    Step 6The tetrahedral intermediate collapses, completing the transfer of ubiquitin from the Cys600 residue of E1 to Cys88 of E2. The active site of E1 is regenerated.
    Step 7The loaded E2 enzyme moves into the E3 active site. The pocket positions the covalently bound ubiquitin in close proximity to an activated lysine residue from a substrate protein. This lysine is then activated towards nucleophilic attack at the thio-ester carbonyl.
    Step 8The tetrahedral intermediate collapses, regenerating the E2 active site and forming a ubiquitinated lysine product. In the absence of a catalytic base, the simultaneous proton transfer has been inferred.

    View similar reactions (composite manual annotation)

    Catalytic Residues Involved

    Type Number Chain Location of Function
    Asn 781 A Main Chain Amide
    Asp 782 A Main Chain Amide
    Arg 603 A Side Chain
    Cys 600 A Side Chain
    Thr 601 A Side Chain
    Cys 88 B Side Chain
    Asp 123 C Side Chain
    Tyr 82 C Side Chain
    Asn 80 C Side Chain
    Arg 481 A Side Chain
    Asp 533 A Side Chain
    Arg 21 A Side Chain

    Metal Cofactors for M0307

    Type Het group Number Chain
    magnesium No Available PDB Information


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      Medline: 19352404
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      Medline: 18662542
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      Medline: 20164921
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      Medline: 11713534
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      Medline: 10558980
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      Medline: 7800044
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      Medline: 10998601
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      Medline: 19684601
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      Medline: 17919899
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      Medline: 19851334
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      Medline: 19940261
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      Medline: 14517261
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      Medline: 20797627
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      Medline: 14998368

    Homologue information for M0307 (3cmm)

    MACiE Homologues (within the PDB)

    MACiE Homologues (within UniprotKB/SwissProt)

    Links to this entry in other databases

    Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
    Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

    GOA logo
    catalytic activity (molecular function)
    binding (molecular function)
    ATP binding (molecular function)
    cellular protein modification process (biological process)
    metabolic process (biological process)
    small protein activating enzyme activity (molecular function)