Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 55486.96 
• Atom Count: 3688 
• Residue Count: 486 
• Unique protein chains: 3

2IO2

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

• DOI: 10.2210/pdb2IO2/pdb

• Classification: PROTEIN BINDING HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2006-10-09 Released: 2006-11-21 
• Deposition Author(s): Reverter, D., Lima, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.301 
• R-Value Work: 0.268 

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

• PubMed: 17099700 
• DOI: 10.1038/nsmb1168
• Primary Citation of Related Structures:  
  2IO3, 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Sentrin-specific protease 2	A	232	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Small ubiquitin-related modifier 1	B	82	Homo sapiens	Mutation(s): 0  Gene Names: SUMO1 (SMT3C, SMT3H3, UBL1)
Find proteins for P63165 (Homo sapiens) Go to Gene View: SUMO1 Go to UniProtKB:  P63165

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Ran GTPase-activating protein 1	C	172	Homo sapiens	Mutation(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: 2.9 Å
• R-Value Free: 0.301 
• R-Value Work: 0.268 
• Space Group: P 6₄ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 163.960	α = 90.00
b = 163.960	β = 90.00
c = 77.770	γ = 120.00

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-09 
• Released Date: 2006-11-21 
• Deposition Author(s): Reverter, D., Lima, C.D.

Revision History 

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