2OG4

Structure of an expanded Jab1-MPN-like domain of splicing factor Prp8p from yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa.

Pena, V.Liu, S.Bujnicki, J.M.Luhrmann, R.Wahl, M.C.

(2007) Mol Cell 25: 615-624

  • DOI: 10.1016/j.molcel.2007.01.023
  • Primary Citation of Related Structures:  
    2OG4

  • PubMed Abstract: 
  • Protein Prp8 interacts with several other spliceosomal proteins, snRNAs, and the pre-mRNA and thereby organizes the active site(s) of the spliceosome. The DEAD-box protein Brr2 and the GTPase Snu114 bind to the Prp8 C terminus, a region where mutatio ...

    Protein Prp8 interacts with several other spliceosomal proteins, snRNAs, and the pre-mRNA and thereby organizes the active site(s) of the spliceosome. The DEAD-box protein Brr2 and the GTPase Snu114 bind to the Prp8 C terminus, a region where mutations in human Prp8 are linked to the RP13 form of Retinitis pigmentosa. We show crystallographically that the C-terminal domain of yeast Prp8p exhibits a Jab1/MPN-like core known from deubiquitinating enzymes. Insertions and terminal appendices are grafted onto this core, covering a putative isopeptidase center whose metal binding site is additionally impaired. Targeted yeast-two-hybrid analyses show that the RP13-linked region in the C-terminal appendix of human Prp8 is essential for binding of human Brr2 and Snu114, and that RP13 point mutations in this fragment weaken these interactions. We conclude that the expanded Prp8 Jab1/MPN domain represents a pseudoenzyme converted into a protein-protein interaction platform and that dysfunction of this platform underlies Retinitis pigmentosa.


    Organizational Affiliation

    AG Röntgenkristallographie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A254Saccharomyces cerevisiae RM11-1aMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33334 
Go to UniProtKB:  P33334
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.465α = 90
b = 78.465β = 90
c = 122.812γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description