2IO1

Crystal structure of human Senp2 in complex with preSUMO-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 

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
  • Structures With Same Primary Citation

  • 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 a ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sentrin-specific protease 2A, C, E232Homo sapiensMutation(s): 1 
Gene Names: SENP2KIAA1331
EC: 3.4.22
Find proteins for Q9HC62 (Homo sapiens)
Explore Q9HC62 
Go to UniProtKB:  Q9HC62
NIH Common Fund Data Resources
PHAROS  Q9HC62
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 3 precursorB, D, F94Homo sapiensMutation(s): 0 
Gene Names: SUMO3SMT3ASMT3H1
Find proteins for P55854 (Homo sapiens)
Explore P55854 
Go to UniProtKB:  P55854
NIH Common Fund Data Resources
PHAROS  P55854
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.98α = 90
b = 143.36β = 90
c = 134.12γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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