9GLT | pdb_00009glt

Crystal Structure of Yeast Ubc13 C87E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.191 (DCC) 

Starting Model: experimental
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Literature

UFC1 reveals the multifactorial and plastic nature of oxyanion holes in E2 conjugating enzymes.

Kumar, M.Banerjee, S.Cohen-Kfir, E.Mitelberg, M.B.Tiwari, S.Isupov, M.N.Dessau, M.Wiener, R.

(2025) Nat Commun 16: 3912-3912

  • DOI: https://doi.org/10.1038/s41467-025-58826-y
  • Primary Citation of Related Structures:  
    9GLH, 9GLI, 9GLJ, 9GLK, 9GLL, 9GLM, 9GLN, 9GLO, 9GLP, 9GLR, 9GLS, 9GLT, 9GMM, 9GMN, 9GN8, 9I9M, 9I9N, 9I9O, 9I9P, 9IA8

  • PubMed Abstract: 

    The conjugation of ubiquitin (Ub) or ubiquitin-like proteins (UBL) to target proteins is a crucial post-translational modification that typically involves nucleophilic attack by a lysine on a charged E2 enzyme (E2~Ub/UBL), forming an oxyanion intermediate. Stabilizing this intermediate through an oxyanion hole is vital for progression of the reaction. Still, the mechanism of oxyanion stabilization in E2 enzymes remains unclear, although an asparagine residue in the conserved HPN motif of E2 enzymes was suggested to stabilize the oxyanion intermediate. Here, we study the E2 enzyme UFC1, which presents a TAK rather than an HPN motif. Crystal structures of UFC1 mutants, including one that mimics the oxyanion intermediate, combined with in vitro activity assays, suggest that UFC1 utilizes two distinct types of oxyanion holes, one that stabilizes the oxyanion intermediate during trans-ufmylation mediated by the E3 ligase, and another that stabilizes cis-driven auto-ufmylation. Our findings indicate that oxyanion stabilization is influenced by multiple factors, including C-alpha hydrogen bonding, and is adaptable, enabling different modes of action.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 13A [auth AAA],
B [auth BBB]
154Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: UBC13YDR092WYD6652.04
EC: 2.3.2.23
UniProt
Find proteins for P52490 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P52490 
Go to UniProtKB:  P52490
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52490
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.603α = 90
b = 127.663β = 96.21
c = 42.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael491/2021

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release