5H2X

Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-172)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the Karyopherins Kap121p and Kap60p Bound to the Nuclear Pore-Targeting Domain of the SUMO Protease Ulp1p

Hirano, H.Kobayashi, J.Matsuura, Y.

(2017) J Mol Biol 429: 249-260

  • DOI: 10.1016/j.jmb.2016.11.029
  • Primary Citation of Related Structures:  
    5H2X, 5H2W, 5H2V

  • PubMed Abstract: 
  • The budding yeast small ubiquitin-like modifier (SUMO) protease Ulp1p catalyzes both the processing of newly synthesized SUMO to its mature form and the deconjugation of SUMO from target proteins, thereby regulating a wide range of cellular processes ...

    The budding yeast small ubiquitin-like modifier (SUMO) protease Ulp1p catalyzes both the processing of newly synthesized SUMO to its mature form and the deconjugation of SUMO from target proteins, thereby regulating a wide range of cellular processes including cell division, DNA repair, DNA replication, transcription, and mRNA quality control. Ulp1p is localized primarily at the nuclear pore complex (NPC) through interactions involving the karyopherins Kap121p and Kap95p-Kap60p heterodimer and a subset of nuclear pore-associated proteins. The sequestration of Ulp1p at the nuclear periphery is crucial for the proper control of protein desumoylation. To gain insights into the role of the karyopherins in regulating the localization of Ulp1p, we have determined the crystal structures of Kap121p and Kap60p bound to the N-terminal non-catalytic domain of Ulp1p that is necessary and sufficient for NPC targeting. Contrary to a previous proposal that Ulp1p is tethered to the transport channel of the NPC through unconventional interactions with the karyopherins, our structures reveal that Ulp1p has canonical nuclear localization signals (NLSs): (1) an isoleucine-lysine-NLS (residues 51-55) that binds to the NLS-binding site of Kap121p, and (2) a classical bipartite NLS (residues 154-172) that binds to the major and minor NLS-binding sites of Kap60p. Ulp1p also binds Kap95p directly, and the Ulp1p-Kap95p binding is enhanced by the importin-β-binding domain of Kap60p. GTP-bound Gsp1p (the yeast Ran ortholog) and the exportin Cse1p cooperate to release Ulp1p from the karyopherins, indicating that the stable sequestration of Ulp1p to the NPC would require a karyopherin-independent mechanism to anchor Ulp1p at the NPC.


    Organizational Affiliation

    Division of Biological Science, Graduate School of Science, Nagoya University, 464-8602, Japan; Structural Biology Research Center, Graduate School of Science, Nagoya University, 464-8602, Japan. Electronic address: matsuura.yoshiyuki@d.mbox.nagoya-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Importin subunit alphaA423Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SRP1KAP60YNL189WN1606
Find proteins for Q02821 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02821 
Go to UniProtKB:  Q02821
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like-specific protease 1B23Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ULP1YPL020CLPB11C
EC: 3.4.22.68
Find proteins for Q02724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02724 
Go to UniProtKB:  Q02724
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.57α = 90
b = 77.48β = 90
c = 114.59γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan25440019

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection