2IO3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.277 

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:  

  • 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 2
A
232Homo sapiensMutation(s): 1 
Gene Names: SENP2 (KIAA1331)
EC: 3.4.22.-
Find proteins for Q9HC62 (Homo sapiens)
Go to Gene View: SENP2
Go to UniProtKB:  Q9HC62
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 2
B
81Homo sapiensMutation(s): 0 
Gene Names: SUMO2 (SMT3B, SMT3H2)
Find proteins for P61956 (Homo sapiens)
Go to Gene View: SUMO2
Go to UniProtKB:  P61956
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ran GTPase-activating protein 1
C
172Homo sapiensMutation(s): 1 
Gene Names: RANGAP1 (KIAA1835, SD)
Find proteins for P46060 (Homo sapiens)
Go to Gene View: RANGAP1
Go to UniProtKB:  P46060
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.277 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 164.056α = 90.00
b = 164.056β = 90.00
c = 78.094γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
ADSCdata collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description