6FX4

Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

beta-Sheet Augmentation Is a Conserved Mechanism of Priming HECT E3 Ligases for Ubiquitin Ligation.

Jackl, M.Stollmaier, C.Strohaker, T.Hyz, K.Maspero, E.Polo, S.Wiesner, S.

(2018) J. Mol. Biol. 430: 3218-3233

  • DOI: 10.1016/j.jmb.2018.06.044
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ubiquitin (Ub) ligases (E3s) catalyze the attachment of Ub chains to target proteins and thereby regulate a wide array of signal transduction pathways in eukaryotes. In HECT-type E3s, Ub first forms a thioester intermediate with a strictly conserved ...

    Ubiquitin (Ub) ligases (E3s) catalyze the attachment of Ub chains to target proteins and thereby regulate a wide array of signal transduction pathways in eukaryotes. In HECT-type E3s, Ub first forms a thioester intermediate with a strictly conserved Cys in the C-lobe of the HECT domain and is then ligated via an isopeptide bond to a Lys residue in the substrate or a preceding Ub in a poly-Ub chain. To date, many key aspects of HECT-mediated Ub transfer have remained elusive. Here, we provide structural and functional insights into the catalytic mechanism of the HECT-type ligase Huwe1 and compare it to the unrelated, K63-specific Smurf2 E3, a member of the Nedd4 family. We found that the Huwe1 HECT domain, in contrast to Nedd4-family E3s, prioritizes K6- and K48-poly-Ub chains and does not interact with Ub in a non-covalent manner. Despite these mechanistic differences, we demonstrate that the architecture of the C-lobe~Ub intermediate is conserved between Huwe1 and Smurf2 and involves a reorientation of the very C-terminal residues. Moreover, in Nedd4 E3s and Huwe1, the individual sequence composition of the Huwe1 C-terminal tail modulates ubiquitination activity, without affecting thioester formation. In sum, our data suggest that catalysis of HECT ligases hold common features, such as the β-sheet augmentation that primes the enzymes for ligation, and variable elements, such as the sequence of the HECT C-terminal tail, that fine-tune ubiquitination activity and may aid in determining Ub chain specificity by positioning the substrate or acceptor Ub.


    Organizational Affiliation

    Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany; Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany.,IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy.,Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany; Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany. Electronic address: silke.wiesner@ur.de.,Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany.,IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Via S. Sofia, 9/1, 20122 Milan, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase SMURF2
A, C
122Homo sapiensMutation(s): 3 
Gene Names: SMURF2
EC: 2.3.2.26
Find proteins for Q9HAU4 (Homo sapiens)
Go to Gene View: SMURF2
Go to UniProtKB:  Q9HAU4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B, D
76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.630α = 108.92
b = 45.950β = 94.43
c = 70.460γ = 106.75
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-18
    Type: Data collection, Structure summary
  • Version 1.2: 2018-08-29
    Type: Data collection, Database references
  • Version 1.3: 2019-03-06
    Type: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary