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Overview for MACiE Entry M0307

Version history

General Information

EC Number: 6.3.2.19 (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:

    • 3.10.20.90 - 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
    C00002
    CHEBI:30616
    Protein lysine
    C02188
    CHEBI:29967
    2 ubiquitin
    C00496
    adenylated ubiquitin
    X00142
    Ubiqutinated protein lysine
    C03635
    2 diphosphate
    C00013
    CHEBI:18361
    AMP
    C00020
    CHEBI:16027

    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

    References

    1. B. A. Schulman et al. (2009), Nat. Rev. Mol. Cell Biol., 10, 319-131. Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways.
      Medline: 19352404
    2. A. L. Haas et al. (1982), J. Biol. Chem., 257, 2543-2548. Ubiquitin-activating enzyme. Mechanism and role in protein-ubiquitin conjugation.
      Medline: 627790
    3. I. Lee et al. (2008), Cell, 134, 268-278. Structural insights into E1-catalyzed ubiquitin activation and transfer to conjugating enzymes.
      Medline: 18662542
    4. C. M. Pickart et al. (2004), Biochim. Biophys. Acta, 1695, 55-72. Ubiquitin: structures, functions, mechanisms.
      Medline: 15571809
    5. S. K. Olsen et al. (2010), Nature, 7283, 906-912. Active site remodelling accompanies thioester bond formation in the SUMO E1.
      Medline: 20164921
    6. M. W. Lake et al. (2001), Nature, 6861, 325-329. Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex.
      Medline: 11713534
    7. L. Huang et al. (1999), Science, 286, 1321-1326. Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade.
      Medline: 10558980
    8. M. Scheffner et al. (1995), Nature, 373, 81-83. Protein ubiquitination involving an E1-E2-E3 enzyme ubiquitin thioester cascade.
      Medline: 7800044
    9. P. K. Jackson et al. (2000), Trends Cell Biol., 10, 429-439. The lore of the RINGs: substrate recognition and catalysis by ubiquitin ligases.
      Medline: 10998601
    10. F. Mohideen et al. (2009), Nat. Struct. Mol. Biol., 16, 945-952. A molecular basis for phosphorylation-dependent SUMO conjugation by the E2 UBC9.
      Medline: 19684601
    11. A. D. Capili et al. (2007), Curr. Opin. Struct. Biol., 17, 826-735. Taking it step by step: mechanistic insights from structural studies of ubiquitin/ubiquitin-like protein modification pathways.
      Medline: 17919899
    12. Y. Ye et al. (2009), Nat. Rev. Mol. Cell Biol., 10, 755-764. Building ubiquitin chains: E2 enzymes at work.
      Medline: 19851334
    13. S. J. van Wijk et al. (2009), FASEB J., 24, 981-993. The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins.
      Medline: 19940261
    14. P. Y. Wu et al. (2003), The EMBO Journal, 22, 5241-5250. A conserved catalytic residue in the ubiquitin-conjugating enzyme family.
      Medline: 14517261
    15. A. A. Yunus et al. (2006), Nat. Struct. Mol. Biol., 13, 491-499. Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.
      Medline: 16732283
    16. D. K. Worthylake et al. (1998), J. Biol. Chem., 273, 6271-6276. Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6 A resolution.
      Medline: 9497353
    17. M. C. Rodrigo-Brenni et al. (2010), Mol. Cell, 39, 548-559. Catalysis of lysine 48-specific ubiquitin chain assembly by residues in E2 and ubiquitin.
      Medline: 20797627
    18. L. A. Passmore et al. (2004), Biochem. J., 379, 513-525. Getting into position: the catalytic mechanisms of protein ubiquitylation.
      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)
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