2G4D

Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of the SENP1 mutant C603S-SUMO complex reveals the hydrolytic mechanism of SUMO-specific protease

Xu, Z., Chau, S.F., Lam, K.H., Chan, H.Y., Ng, T.B., Au, S.W.N.

(2006) Biochem J 398: 345-352

  • DOI: 10.1042/BJ20060526
  • Primary Citation of Related Structures:  
    2G4D

  • PubMed Abstract: 

    • SUMO (small ubiquitin-related modifier)-specific proteases catalyse the maturation and de-conjugation processes of the sumoylation pathway and modulate various cellular responses including nuclear metabolism and cell cycle progression. The active-site cysteine residue is conserved among all known SUMO-specific proteases and is not substitutable by serine in the hydrolysis reactions demonstrated previously in yeast ...

    SUMO (small ubiquitin-related modifier)-specific proteases catalyse the maturation and de-conjugation processes of the sumoylation pathway and modulate various cellular responses including nuclear metabolism and cell cycle progression. The active-site cysteine residue is conserved among all known SUMO-specific proteases and is not substitutable by serine in the hydrolysis reactions demonstrated previously in yeast. We report here that the catalytic domain of human protease SENP1 (SUMO-specific protease 1) mutant SENP1C(C603S) carrying a mutation of cysteine to serine at the active site is inactive in maturation and de-conjugation reactions. To further understand the hydrolytic mechanism catalysed by SENP1, we have determined, at 2.8 A resolution (1 A = 0.1 nm), the X-ray structure of SENP1C(C603S)-SUMO-1 complex. A comparison of the structure of SENP2-SUMO-1 suggests strongly that SUMO-specific proteases require a self-conformational change prior to cleavage of peptide or isopeptide bond in the maturation and de-conjugation processes respectively. Moreover, analysis of the interface of SENP1 and SUMO-1 has led to the identification of four unique amino acids in SENP1 that facilitate the binding of SUMO-1. By means of an in vitro assay, we further demonstrate a novel function of SENP1 in hydrolysing the thioester linkage in E1-SUMO and E2-SUMO complexes. The results disclose a new mechanism of regulation of the sumoylation pathway by the SUMO-specific proteases.

    Related Citations: 
    • Mapping residues of SUMO precursors essential in differential maturation by SUMO-specific protease, SENP1
      Xu, Z., Au, S.W.N.
      (2005) Biochem J 386: 325
    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biotechnology Program, Centre for Protein Science and Crystallography, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SENP1 protein A, C205Homo sapiensMutation(s): 1 
Gene Names: SENP1
EC: 3.4.22
Find proteins for Q9P0U3 (Homo sapiens)
Explore Q9P0U3 
Go to UniProtKB:  Q9P0U3
NIH Common Fund Data Resources
PHAROS:  Q9P0U3
GTEx:  ENSG00000079387
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1 B, D78Homo sapiensMutation(s): 0 
Gene Names: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS:  P63165
GTEx:  ENSG00000116030
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.308α = 90
b = 97.308β = 90
c = 102.58γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description