3GOE

Molecular Mimicry of SUMO promotes DNA repair

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.145 

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This is version 1.1 of the entry. See complete history. 


Literature

Molecular mimicry of SUMO promotes DNA repair.

Prudden, J., Perry, J.J., Arvai, A.S., Tainer, J.A., Boddy, M.N.

(2009) Nat Struct Mol Biol 16: 509-516

  • DOI: 10.1038/nsmb.1582
  • Primary Citation of Related Structures:  
    3GOE

  • PubMed Abstract: 

    • Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). We show here that despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes ...

    Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). We show here that despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. The molecular basis of this selectivity is revealed by our 0.97-A resolution crystal structure of Rad60 SLD2, which shows that apart from the conserved non-substrate SUMO:Ubc9 interface, the surface features of SLD2 are distinct from those of SUMO. Abrogation of the SLD2:Ubc9 FEG motif-dependent interaction results in hypersensitivity to genotoxic stress and an increase in spontaneous recombination associated with aberrant replication forks. Our results provide a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating sumoylation.

    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein rad60A82Schizosaccharomyces pombeMutation(s): 0 
Gene Names: rad60, SPBC1921.02
UniProt
Find proteins for Q9USX3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9USX3 
Go to UniProtKB:  Q9USX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9USX3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.145 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.519α = 90
b = 81.519β = 90
c = 81.519γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-03-19 
  • Released Date: 2009-04-14 
    • Deposition Author(s): Perry, J.J.P.

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance