7R2E

Structure of human Senp7 with SUMO2

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

  • Deposited: 2022-02-04 Released: 2022-12-07 
  • Deposition Author(s): Reverter, D., Li, Y.
  • Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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This is version 2.1 of the entry. See complete history


Literature

Structural Basis for the SUMO2 Isoform Specificity of SENP7.

Li, Y.De Bolos, A.Amador, V.Reverter, D.

(2022) J Mol Biol 434: 167875-167875

  • DOI: https://doi.org/10.1016/j.jmb.2022.167875
  • Primary Citation of Related Structures:  
    7R2E

  • PubMed Abstract: 

    SUMO proteases or deSUMOylases regulate the lifetime of SUMO-conjugated targets in the cell by cleaving off the isopetidic bond between the substrate and the SUMO modifier, thus reversing the conjugation activity of the SUMO E3 ligases. In humans the deSUMOylating activity is mainly conducted by the SENP/ULP protease family, which is constituted of six members sharing a homologous catalytic globular domain. SENP6 and SENP7 are the most divergent members of the family and they show a unique SUMO2/3 isoform preference and a particular activity for dismantling polySUMO2 chains. Here, we present the crystal structure of the catalytic domain of human SENP7 bound to SUMO2, revealing structural key elements for the SUMO2 isoform specificity of SENP7. In particular, we describe the specific contacts between SUMO2 and a unique insertion in SENP7 (named Loop1) that is responsible for the SUMO2 isoform specificity. All the other interface contacts between SENP7 and SUMO2, including the SUMO2 C-terminal tail interaction, are conserved among members of the SENP/ULP family. Our data give insight into an evolutionary adaptation to restrict the deSUMOylating activity in SENP6 and SENP7 for the SUMO2/3 isoforms.


  • Organizational Affiliation

    Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sentrin-specific protease 7
A, B
345Homo sapiensMutation(s): 0 
Gene Names: SENP7KIAA1707SSP2SUSP2
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQF6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 3
C, D
76Homo sapiensMutation(s): 0 
Gene Names: SUMO3SMT3ASMT3H1
UniProt & NIH Common Fund Data Resources
Find proteins for P55854 (Homo sapiens)
Explore P55854 
Go to UniProtKB:  P55854
PHAROS:  P55854
GTEx:  ENSG00000184900 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55854
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.413α = 90
b = 100.73β = 90.28
c = 93.037γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 2.0: 2023-03-01
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-02-07
    Changes: Data collection, Refinement description