5EJJ

Crystal structure of UfSP from C.elegans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The MPN domain of Caenorhabditis elegans UfSP modulates both substrate recognition and deufmylation activity

Ha, B.H.Kim, K.H.Yoo, H.M.Lee, W.Kim, E.E.

(2016) Biochem Biophys Res Commun 476: 450-456

  • DOI: https://doi.org/10.1016/j.bbrc.2016.05.143
  • Primary Citation of Related Structures:  
    5EJJ

  • PubMed Abstract: 

    Ubiquitin-fold modifier 1 (Ufm1) specific protease (UfSP) is a novel cysteine protease that activates Ufm1 from its precursor by processing the C-terminus to expose the conserved Gly necessary for substrate conjugation and de-conjugates Ufm1 from the substrate. There are two forms: UfSP1 and UfSP2, the later with an additional domain at the N-terminus. Ufm1 and both the conjugating and deconjugating enzymes are highly conserved. However, in Caenorhabditis elegans there is one UfSP which has extra 136 residues at the N terminus compared to UfSP2. The crystal structure of cUfSP reveals that these additional residues display a MPN fold while the rest of the structure mimics that of UfSP2. The MPN domain does not have the metalloprotease activity found in some MPN-domain containing protein, rather it is required for the recognition and deufmylation of the substrate of cUfSP, UfBP1. In addition, the MPN domain is also required for localization to the endoplasmic reticulum.


  • Organizational Affiliation

    Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ufm1-specific protease
A, B
564Caenorhabditis elegansMutation(s): 0 
Gene Names: odr-8ufsp-2F38A5.1
EC: 3.4.22
UniProt
Find proteins for Q94218 (Caenorhabditis elegans)
Explore Q94218 
Go to UniProtKB:  Q94218
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94218
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.531α = 90
b = 149.808β = 90
c = 226.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
SOLVEphasing
RESOLVEphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science, ICT and Future PlanningKorea, Republic OfNRF 20110021713

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references