7NVK

Crystal structure of UBA5 fragment fused to the N-terminus of UFC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for UFM1 transfer from UBA5 to UFC1.

Kumar, M.Padala, P.Fahoum, J.Hassouna, F.Tsaban, T.Zoltsman, G.Banerjee, S.Cohen-Kfir, E.Dessau, M.Rosenzweig, R.Isupov, M.N.Schueler-Furman, O.Wiener, R.

(2021) Nat Commun 12: 5708-5708

  • DOI: https://doi.org/10.1038/s41467-021-25994-6
  • Primary Citation of Related Structures:  
    7NVJ, 7NVK, 7NW1

  • PubMed Abstract: 

    Ufmylation is a post-translational modification essential for regulating key cellular processes. A three-enzyme cascade involving E1, E2 and E3 is required for UFM1 attachment to target proteins. How UBA5 (E1) and UFC1 (E2) cooperatively activate and transfer UFM1 is still unclear. Here, we present the crystal structure of UFC1 bound to the C-terminus of UBA5, revealing how UBA5 interacts with UFC1 via a short linear sequence, not observed in other E1-E2 complexes. We find that UBA5 has a region outside the adenylation domain that is dispensable for UFC1 binding but critical for UFM1 transfer. This region moves next to UFC1's active site Cys and compensates for a missing loop in UFC1, which exists in other E2s and is needed for the transfer. Overall, our findings advance the understanding of UFM1's conjugation machinery and may serve as a basis for the development of ufmylation inhibitors.


  • 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-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1A [auth AAA]226Homo sapiensMutation(s): 0 
Gene Names: UBA5UBE1DC1UFC1CGI-126HSPC155
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3C8 (Homo sapiens)
Explore Q9Y3C8 
Go to UniProtKB:  Q9Y3C8
PHAROS:  Q9Y3C8
GTEx:  ENSG00000143222 
Find proteins for Q9GZZ9 (Homo sapiens)
Explore Q9GZZ9 
Go to UniProtKB:  Q9GZZ9
PHAROS:  Q9GZZ9
GTEx:  ENSG00000081307 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9GZZ9Q9Y3C8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.63α = 90
b = 84.63β = 90
c = 60.77γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael1383/17

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description