2CKH

SENP1-SUMO2 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The Structure of Senp1-Sumo-2 Complex Suggests a Structural Basis for Discrimination between Sumo Paralogues During Processing.

Shen, L.N., Dong, C., Liu, H., Naismith, J.H., Hay, R.T.

(2006) Biochem J 397: 279

  • DOI: 10.1042/BJ20052030
  • Primary Citation of Related Structures:  
    2CKH, 2CKG

  • PubMed Abstract: 

    • The SUMO (small ubiquitin-like modifier)-specific protease SENP1 (sentrin-specific protease 1) can process the three forms of SUMO to their mature forms and deconjugate SUMO from modified substrates. It has been demonstrated previously that SENP1 processed SUMO-1 more efficiently than SUMO-2, but displayed little difference in its ability to deconjugate the different SUMO paralogues from modified substrates ...

    The SUMO (small ubiquitin-like modifier)-specific protease SENP1 (sentrin-specific protease 1) can process the three forms of SUMO to their mature forms and deconjugate SUMO from modified substrates. It has been demonstrated previously that SENP1 processed SUMO-1 more efficiently than SUMO-2, but displayed little difference in its ability to deconjugate the different SUMO paralogues from modified substrates. To determine the basis for this substrate specificity, we have determined the crystal structure of SENP1 in isolation and in a transition-state complex with SUMO-2. The interface between SUMO-2 and SENP1 has a relatively poor complementarity, and most of the recognition is determined by interaction between the conserved C-terminus of SUMO-2 and the cleft in the protease. Although SENP1 is rather similar in structure to the related protease SENP2, these proteases have different SUMO-processing activities. Electrostatic analysis of SENP1 in the region where the C-terminal peptide, removed during maturation, would project indicates that it is the electrostatic complementarity between this region of SENP1 and the C-terminal peptides of the various SUMO paralogues that mediates selectivity.

    Organizational Affiliation: 

    Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland KY16 9ST, UK.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SENTRIN-SPECIFIC PROTEASE 1A225Homo sapiensMutation(s): 0 
Gene Names: SENP1
EC: 3.4.22
Find proteins for Q9P0U3 (Homo sapiens)
Explore Q9P0U3 
Go to UniProtKB:  Q9P0U3
NIH Common Fund Data Resources
PHAROS:  Q9P0U3
GTEx:  ENSG00000079387
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SMALL UBIQUITIN-RELATED MODIFIER 2B79Homo sapiensMutation(s): 0 
Gene Names: SUMO2, SMT3B, SMT3H2
Find proteins for P61956 (Homo sapiens)
Explore P61956 
Go to UniProtKB:  P61956
NIH Common Fund Data Resources
PHAROS:  P61956
GTEx:  ENSG00000188612
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.249 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.376α = 90
b = 143.376β = 90
c = 71.886γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-08-30
    Changes: Data collection, Refinement description