2IO3

Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates.

Reverter, D.Lima, C.D.

(2006) Nat Struct Mol Biol 13: 1060-1068

  • DOI: https://doi.org/10.1038/nsmb1168
  • Primary Citation of Related Structures:  
    2IO0, 2IO1, 2IO2, 2IO3

  • PubMed Abstract: 

    SUMO processing and deconjugation are essential proteolytic activities for nuclear metabolism and cell-cycle progression in yeast and higher eukaryotes. To elucidate the mechanisms used during substrate lysine deconjugation, SUMO isoform processing and SUMO isoform interactions, X-ray structures were determined for a catalytically inert SENP2 protease domain in complex with conjugated RanGAP1-SUMO-1 or RanGAP1-SUMO-2, or in complex with SUMO-2 or SUMO-3 precursors. Common features within the active site include a 90 degrees kink proximal to the scissile bond that forces C-terminal amino acid residues or the lysine side chain toward a protease surface that appears optimized for lysine deconjugation. Analysis of this surface reveals SENP2 residues, particularly Met497, that mediate, and in some instances reverse, in vitro substrate specificity. Mutational analysis and biochemistry provide a mechanism for SENP2 substrate preferences that explains why SENP2 catalyzes SUMO deconjugation more efficiently than processing.


  • Organizational Affiliation

    Structural Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sentrin-specific protease 2232Homo sapiensMutation(s): 1 
Gene Names: SENP2KIAA1331
EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC62 (Homo sapiens)
Explore Q9HC62 
Go to UniProtKB:  Q9HC62
PHAROS:  Q9HC62
GTEx:  ENSG00000163904 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HC62
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 281Homo sapiensMutation(s): 0 
Gene Names: SUMO2SMT3BSMT3H2
UniProt & NIH Common Fund Data Resources
Find proteins for P61956 (Homo sapiens)
Explore P61956 
Go to UniProtKB:  P61956
PHAROS:  P61956
GTEx:  ENSG00000188612 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61956
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ran GTPase-activating protein 1172Homo sapiensMutation(s): 1 
Gene Names: RANGAP1
UniProt & NIH Common Fund Data Resources
Find proteins for P46060 (Homo sapiens)
Explore P46060 
Go to UniProtKB:  P46060
PHAROS:  P46060
GTEx:  ENSG00000100401 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46060
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.056α = 90
b = 164.056β = 90
c = 78.094γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description