2IO2

Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.268 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 10.1038/nsmb1168
  • Primary Citation of Related Structures:  
    2IO3, 2IO2, 2IO1, 2IO0

  • 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Sentrin-specific protease 2A232Homo sapiensMutation(s): 1 
Gene Names: SENP2KIAA1331
EC: 3.4.22
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Find proteins for Q9HC62 (Homo sapiens)
Explore Q9HC62 
Go to UniProtKB:  Q9HC62
PHAROS:  Q9HC62
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1B82Homo sapiensMutation(s): 0 
Gene Names: SUMO1SMT3CSMT3H3UBL1OK/SW-cl.43
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Find proteins for P63165 (Homo sapiens)
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PHAROS:  P63165
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ran GTPase-activating protein 1C172Homo sapiensMutation(s): 1 
Gene Names: RANGAP1KIAA1835SD
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Find proteins for P46060 (Homo sapiens)
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Go to UniProtKB:  P46060
PHAROS:  P46060
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.268 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.96α = 90
b = 163.96β = 90
c = 77.77γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description