2WP7 | pdb_00002wp7

Crystal structure of deSUMOylase(DUF862)

• PDB DOI: https://doi.org/10.2210/pdb2WP7/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-03 Released: 2010-09-01 
• Deposition Author(s): Kim, J.H., Woo, J.S., Oh, B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.228 (Depositor) 
• R-Value Work: 
  0.223 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Desi-1, a Novel Desumoylase Belonging to a Putative Isopeptidase Superfamily.

Suh, H.Y., Kim, J.H., Woo, J.S., Ku, B., Shin, E.J., Yun, Y., Oh, B.H.

(2012) Proteins 80: 2099

• PubMed: 22498933 
• DOI: https://doi.org/10.1002/prot.24093
• Primary Citation Related Structures: 
  2WP7


• PubMed Abstract: 
  

  Post-translational modification by small ubiquitin-like modifier (SUMO) can be reversed by sentrin/SUMO-specific proteases (SENPs), the first known class of deSUMOylase. Recently, we identified a new deSUMOylating enzyme DeSI-1, which is distinct from SENPs and belongs to the putative deubiquitinating isopeptidase PPPDE superfamily. Herein, we report the crystal structure of DeSI-1, revealing that this enzyme forms a homodimer and that the groove between the two subunits is the active site harboring two absolutely conserved cysteine and histidine residues that form a catalytic dyad. We also show that DeSI-1 exhibits an extremely low endopeptidase activity toward precursor forms of SUMO-1 and SUMO-2, unlike SENPs.

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Organizational Affiliation: 
• Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.4 kDa 
• Atom Count: 1,278 
• Modeled Residue Count: 159 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PPPDE PEPTIDASE DOMAIN-CONTAINING PROTEIN 2	A	168	Mus musculus	Mutation(s): 0  EC: 3.4.22 (PDB Primary Data), 3.4 (UniProt), 3.1.2.22 (UniProt)
UniProt
Find proteins for Q9CQT7 (Mus musculus) Explore Q9CQT7  Go to UniProtKB:  Q9CQT7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.228 (Depositor) 
• R-Value Work:  0.223 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.033	α = 90
b = 42.033	β = 90
c = 164.514	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Kim, J.H., Woo, J.S., Oh, B.H.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Atomic model, Database references, Version format compliance
• Version 1.2: 2012-07-18
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description