Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 35.87 kDa 
• Atom Count: 2515 
• Modelled Residue Count: 304 
• Deposited Residue Count: 304 
• Unique protein chains: 2

2CKH

SENP1-SUMO2 complex

• PDB DOI: 10.2210/pdb2CKH/pdb
• Entry: 2CKH supersedes: 2BZO

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


• Deposited: 2006-04-18 Released: 2006-04-26 
• Deposition Author(s): Shen, L.N., Dong, C., Liu, H., Hay, R.T., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.294 
• R-Value Work: 0.245 
• R-Value Observed: 0.249 

Literature

The Structure of Senp1-Sumo-2 Complex Suggests a Structural Basis for Discrimination between Sumo Paralogues During Processing.

Shen, L.N., Dong, C., Liu, H., Naismith, J.H., Hay, R.T.

(2006) Biochem J 397: 279

• PubMed: 16553580 
• DOI: 10.1042/BJ20052030
• Primary Citation of Related Structures:  
  2CKG, 2CKH


• PubMed Abstract: 
  

The SUMO (small ubiquitin-like modifier)-specific protease SENP1 (sentrin-specific protease 1) can process the three forms of SUMO to their mature forms and deconjugate SUMO from modified substrates. It has been demonstrated previously that SENP1 processed SUMO-1 more efficiently than SUMO-2, but displayed little difference in its ability to deconjugate the different SUMO paralogues from modified substrates. To determine the basis for this substrate specificity, we have determined the crystal structure of SENP1 in isolation and in a transition-state complex with SUMO-2. The interface between SUMO-2 and SENP1 has a relatively poor complementarity, and most of the recognition is determined by interaction between the conserved C-terminus of SUMO-2 and the cleft in the protease. Although SENP1 is rather similar in structure to the related protease SENP2, these proteases have different SUMO-processing activities. Electrostatic analysis of SENP1 in the region where the C-terminal peptide, removed during maturation, would project indicates that it is the electrostatic complementarity between this region of SENP1 and the C-terminal peptides of the various SUMO paralogues that mediates selectivity.

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Organizational Affiliation: 

Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland KY16 9ST, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SENTRIN-SPECIFIC PROTEASE 1	A	225	Homo sapiens	Mutation(s): 0  Gene Names: SENP1 EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0U3 (Homo sapiens) Explore Q9P0U3  Go to UniProtKB:  Q9P0U3
PHAROS:  Q9P0U3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SMALL UBIQUITIN-RELATED MODIFIER 2	B	79	Homo sapiens	Mutation(s): 0  Gene Names: SUMO2, SMT3B, SMT3H2
UniProt & NIH Common Fund Data Resources
Find proteins for P61956 (Homo sapiens) Explore P61956  Go to UniProtKB:  P61956
PHAROS:  P61956

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.294 
• R-Value Work: 0.245 
• R-Value Observed: 0.249 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.376	α = 90
b = 143.376	β = 90
c = 71.886	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-18 
• Released Date: 2006-04-26 
Deposition Author(s): Shen, L.N., Dong, C., Liu, H., Hay, R.T., Naismith, J.H.
• This entry supersedes: 2BZO

Revision History  

• Version 1.0: 2006-04-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-08-30
  Changes: Data collection, Refinement description