7P47

Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the E3 ligase activity enhancement of yeast Nse2 by SUMO-interacting motifs.

Varejao, N.Lascorz, J.Codina-Fabra, J.Belli, G.Borras-Gas, H.Torres-Rosell, J.Reverter, D.

(2021) Nat Commun 12: 7013-7013

  • DOI: https://doi.org/10.1038/s41467-021-27301-9
  • Primary Citation of Related Structures:  
    7P47

  • PubMed Abstract: 

    Post-translational modification of proteins by ubiquitin and ubiquitin-like modifiers, such as SUMO, are key events in protein homeostasis or DNA damage response. Smc5/6 is a nuclear multi-subunit complex that participates in the recombinational DNA repair processes and is required in the maintenance of chromosome integrity. Nse2 is a subunit of the Smc5/6 complex that possesses SUMO E3 ligase activity by the presence of a SP-RING domain that activates the E2~SUMO thioester for discharge on the substrate. Here we present the crystal structure of the SUMO E3 ligase Nse2 in complex with an E2-SUMO thioester mimetic. In addition to the interface between the SP-RING domain and the E2, the complex reveals how two SIM (SUMO-Interacting Motif) -like motifs in Nse2 are restructured upon binding the donor and E2-backside SUMO during the E3-dependent discharge reaction. Both SIM interfaces are essential in the activity of Nse2 and are required to cope with DNA damage.


  • Organizational Affiliation

    Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 5A [auth B]84Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SMC5YOL034W
UniProt
Find proteins for Q08204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08204 
Go to UniProtKB:  Q08204
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08204
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9B [auth C]165Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: UBC9YDL064W
EC: 2.3.2
UniProt
Find proteins for P50623 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50623 
Go to UniProtKB:  P50623
Entity Groups  
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UniProt GroupP50623
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E3 SUMO-protein ligase MMS21C [auth A]214Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MMS21NSE2YEL019C
EC: 2.3.2
UniProt
Find proteins for P38632 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38632 
Go to UniProtKB:  P38632
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UniProt GroupP38632
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3D [auth E],
E [auth D]
121Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SMT3YDR510WD9719.15
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
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UniProt GroupQ12306
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.144α = 90
b = 103.24β = 90
c = 115.616γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPGC2018-098423-B-I00

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2022-06-08
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description