2IY0

SENP1 (mutant) SUMO1 RanGAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sumo Protease Senp1 Induces Isomerization of the Scissile Peptide Bond.

Shen, L.Tatham, M.H.Dong, C.Zagorska, A.Naismith, J.H.Hay, R.T.

(2006) Nat.Struct.Mol.Biol. 13: 1069

  • DOI: 10.1038/nsmb1172
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small ubiquitin-like modifier (SUMO)-specific protease SENP1 processes SUMO-1, SUMO-2 and SUMO-3 to mature forms and deconjugates them from modified proteins. To establish the proteolytic mechanism, we determined structures of catalytically inactive ...

    Small ubiquitin-like modifier (SUMO)-specific protease SENP1 processes SUMO-1, SUMO-2 and SUMO-3 to mature forms and deconjugates them from modified proteins. To establish the proteolytic mechanism, we determined structures of catalytically inactive SENP1 bound to SUMO-1-modified RanGAP1 and to unprocessed SUMO-1. In each case, the scissile peptide bond is kinked at a right angle to the C-terminal tail of SUMO-1 and has the cis configuration of the amide nitrogens. SENP1 preferentially processes SUMO-1 over SUMO-2, but binding thermodynamics of full-length SUMO-1 and SUMO-2 to SENP1 and K(m) values for processing are very similar. However, k(cat) values differ by 50-fold. Thus, discrimination between unprocessed SUMO-1 and SUMO-2 by SENP1 is based on a catalytic step rather than substrate binding and is likely to reflect differences in the ability of SENP1 to correctly orientate the scissile bonds in SUMO-1 and SUMO-2.


    Organizational Affiliation

    Centre for Interdisciplinary Research, School of Life Science, University of Dundee, DD1 5EH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SENTRIN-SPECIFIC PROTEASE 1
A
226Homo sapiensMutation(s): 1 
Gene Names: SENP1
EC: 3.4.22.-
Find proteins for Q9P0U3 (Homo sapiens)
Go to Gene View: SENP1
Go to UniProtKB:  Q9P0U3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SMALL UBIQUITIN-RELATED MODIFIER 1
B
82Homo sapiensMutation(s): 0 
Gene Names: SUMO1 (SMT3C, SMT3H3, UBL1)
Find proteins for P63165 (Homo sapiens)
Go to Gene View: SUMO1
Go to UniProtKB:  P63165
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RAN GTPASE-ACTIVATING PROTEIN 1
C
156Homo sapiensMutation(s): 0 
Gene Names: RANGAP1 (KIAA1835, SD)
Find proteins for P46060 (Homo sapiens)
Go to Gene View: RANGAP1
Go to UniProtKB:  P46060
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.228 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.380α = 90.00
b = 83.380β = 90.00
c = 148.044γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-06-28
    Type: Data collection