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 
  • R-Value Observed: 0.230 

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
  • Structures With Same Primary Citation

  • 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 1A226Homo 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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SMALL UBIQUITIN-RELATED MODIFIER 1B82Homo sapiensMutation(s): 0 
Gene Names: SUMO1SMT3CSMT3H3UBL1OK/SW-cl.43
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS  P63165
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RAN GTPASE-ACTIVATING PROTEIN 1C156Homo sapiensMutation(s): 0 
Gene Names: RANGAP1KIAA1835SD
Find proteins for P46060 (Homo sapiens)
Explore P46060 
Go to UniProtKB:  P46060
NIH Common Fund Data Resources
PHAROS  P46060
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.38α = 90
b = 83.38β = 90
c = 148.044γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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