5HKH

Crystal structure of Ufm1 in complex with UBA5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation.

Habisov, S.Huber, J.Ichimura, Y.Akutsu, M.Rogova, N.Loehr, F.McEwan, D.G.Johansen, T.Dikic, I.Doetsch, V.Komatsu, M.Rogov, V.V.Kirkin, V.

(2016) J.Biol.Chem. 291: 9025-9041

  • DOI: 10.1074/jbc.M116.715474

  • PubMed Abstract: 
  • The covalent conjugation of ubiquitin-fold modifier 1 (UFM1) to proteins generates a signal that regulates transcription, response to cell stress, and differentiation. Ufmylation is initiated by ubiquitin-like modifier activating enzyme 5 (UBA5), whi ...

    The covalent conjugation of ubiquitin-fold modifier 1 (UFM1) to proteins generates a signal that regulates transcription, response to cell stress, and differentiation. Ufmylation is initiated by ubiquitin-like modifier activating enzyme 5 (UBA5), which activates and transfers UFM1 to ubiquitin-fold modifier-conjugating enzyme 1 (UFC1). The details of the interaction between UFM1 and UBA5 required for UFM1 activation and its downstream transfer are however unclear. In this study, we described and characterized a combined linear LC3-interacting region/UFM1-interacting motif (LIR/UFIM) within the C terminus of UBA5. This single motif ensures that UBA5 binds both UFM1 and light chain 3/γ-aminobutyric acid receptor-associated proteins (LC3/GABARAP), two ubiquitin (Ub)-like proteins. We demonstrated that LIR/UFIM is required for the full biological activity of UBA5 and for the effective transfer of UFM1 onto UFC1 and a downstream protein substrate both in vitro and in cells. Taken together, our study provides important structural and functional insights into the interaction between UBA5 and Ub-like modifiers, improving the understanding of the biology of the ufmylation pathway.


    Organizational Affiliation

    From Translational Innovation Platform Oncology, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany, the Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, the BMLS Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-fold modifier 1
A, C
86Homo sapiensGene Names: UFM1 (C13orf20)
Find proteins for P61960 (Homo sapiens)
Go to Gene View: UFM1
Go to UniProtKB:  P61960
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ASP-ASN-GLU-TRP-GLY-ILE-GLU-LEU-VAL
B
9Homo sapiensGene Names: UBA5 (UBE1DC1)
Find proteins for Q9GZZ9 (Homo sapiens)
Go to Gene View: UBA5
Go to UniProtKB:  Q9GZZ9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.656α = 90.00
b = 82.656β = 90.00
c = 62.027γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references