6UYV

Crystal structure of K46-acetylated SUMO1 in complex with phosphorylated PML-SIM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.401 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Acetylation of SUMO1 Alters Interactions with the SIMs of PML and Daxx in a Protein-Specific Manner.

Mascle, X.H.Gagnon, C.Wahba, H.M.Lussier-Price, M.Cappadocia, L.Sakaguchi, K.Omichinski, J.G.

(2020) Structure 28: 157-168.e5

  • DOI: 10.1016/j.str.2019.11.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The interactions between SUMO proteins and SUMO-interacting motif (SIM) in nuclear bodies formed by the promyelocytic leukemia (PML) protein (PML-NBs) have been shown to be modulated by either phosphorylation of the SIMs or acetylation of SUMO protei ...

    The interactions between SUMO proteins and SUMO-interacting motif (SIM) in nuclear bodies formed by the promyelocytic leukemia (PML) protein (PML-NBs) have been shown to be modulated by either phosphorylation of the SIMs or acetylation of SUMO proteins. However, little is known about how this occurs at the atomic level. In this work, we examined the role that acetylation of SUMO1 plays on its binding to the phosphorylated SIMs (phosphoSIMs) of PML and Daxx. Our results demonstrate that SUMO1 binding to the phosphoSIM of either PML or Daxx is dramatically reduced by acetylation at either K39 or K46. However, acetylation at K37 only impacts binding to Daxx. Structures of acetylated SUMO1 variants bound to the phosphoSIMs of PML and Daxx demonstrate that there is structural plasticity in SUMO-SIM interactions. The plasticity observed in these structures provides a robust mechanism for regulating SUMO-SIM interactions in PML-NBs using signaling generated post-translational modifications.


    Organizational Affiliation

    Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada. Electronic address: jg.omichinski@umontreal.ca.,Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada.,Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada; Department of Biochemistry, Beni-Suef University, Beni-Suef 62521, Egypt.,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 1
A
83Homo sapiensMutation(s): 1 
Gene Names: SUMO1 (SMT3C, SMT3H3, UBL1)
Find proteins for P63165 (Homo sapiens)
Go to Gene View: SUMO1
Go to UniProtKB:  P63165
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein PML
B
29Homo sapiensMutation(s): 1 
Gene Names: PML (MYL, PP8675, RNF71, TRIM19)
Find proteins for P29590 (Homo sapiens)
Go to Gene View: PML
Go to UniProtKB:  P29590
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.401 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.205α = 90.00
b = 46.919β = 90.00
c = 63.624γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada74739
Canadian Institutes of Health Research (CIHR)Canada130414

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-01-08
    Type: Author supporting evidence, Database references
  • Version 1.2: 2020-02-19
    Type: Database references