3EAY | pdb_00003eay

Crystal structure of the human SENP7 catalytic domain

• PDB DOI: https://doi.org/10.2210/pdb3EAY/pdb

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


• Deposited: 2008-08-26 Released: 2008-09-16 
• Deposition Author(s): Lima, C.D., Reverter, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.256 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 

Literature

Structure of the Human SENP7 Catalytic Domain and Poly-SUMO Deconjugation Activities for SENP6 and SENP7.

Lima, C.D., Reverter, D.

(2008) J Biological Chem 283: 32045-32055

• PubMed: 18799455 
• DOI: https://doi.org/10.1074/jbc.M805655200
• Primary Citation Related Structures: 
  3EAY


• PubMed Abstract: 
  

  Small ubiquitin-like modifier (SUMO) proteases regulate the abundance and lifetime of SUMO-conjugated substrates by antagonizing reactions catalyzed by SUMO-conjugating enzymes. Six SUMO proteases constitute the human SENP/ULP protease family (SENP1-3 and SENP5-7). SENP6 and SENP7 include the most divergent class of SUMO proteases, which also includes the yeast enzyme ULP2. We present the crystal structure of the SENP7 catalytic domain at a resolution of 2.4 angstroms. Comparison with structures of human SENP1 and SENP2 reveals unique elements that differ from previously characterized structures of SUMO-deconjugating enzymes. Biochemical assays show that SENP6 and SENP7 prefer SUMO2 or SUMO3 in deconjugation reactions with rates comparable with those catalyzed by SENP2, particularly during cleavage of di-SUMO2, di-SUMO3, and poly-SUMO chains composed of SUMO2 or SUMO3. In contrast, SENP6 and SENP7 exhibit lower rates for processing pre-SUMO1, pre-SUMO2, or pre-SUMO3 in comparison with SENP2. Structure-guided mutational analysis reveals elements unique to the SENP6 and SENP7 subclass of SENP/ULP proteases that contribute to protease function during deconjugation of poly-SUMO chains.

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Organizational Affiliation: 
• Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 37.93 kDa 
• Atom Count: 2,129 
• Modeled Residue Count: 247 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sentrin-specific protease 7	A	323	Homo sapiens	Mutation(s): 0  Gene Names: SENP7, KIAA1707, SSP2, SUSP2 EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQF6 (Homo sapiens) Explore Q9BQF6  Go to UniProtKB:  Q9BQF6
PHAROS:  Q9BQF6 GTEx:  ENSG00000138468

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.256 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.22	α = 90
b = 76.22	β = 90
c = 103.46	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Lima, C.D., Reverter, D.

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations