4LJY

Crystal structure of RNA splicing effector Prp5 in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Literature

Crystal structure of Prp5p reveals interdomain interactions that impact spliceosome assembly.

Zhang, Z.M.Yang, F.Zhang, J.Tang, Q.Li, J.Gu, J.Zhou, J.Xu, Y.Z.

(2013) Cell Rep 5: 1269-1278

  • DOI: https://doi.org/10.1016/j.celrep.2013.10.047
  • Primary Citation of Related Structures:  
    4LJY, 4LK2

  • PubMed Abstract: 

    The DEAD-box adenosine triphosphatase (ATPase) Prp5p facilitates U2 small nuclear ribonucleoprotein particle (snRNP) binding to the intron branch site region during spliceosome assembly. We present crystal structures of S. cerevisiae Prp5p alone and in complex with ADP at 2.12 Å and 1.95 Å resolution. The three-dimensional packing of Prp5p subdomains differs strikingly from that so far observed in other DEAD-box proteins: two RecA-like subdomains adopt an "open state" conformation stabilized by extensive interactions involving sequences that flank the two subdomains. This conformation is distinct from that required for ATP hydrolysis. Consistent with this, Prp5p mutations that destabilize interdomain interactions exhibited increased ATPase activity in vitro and inhibited splicing of suboptimal branch site substrates in vivo, whereas restoration of interdomain interactions reversed these effects. We conclude that the Prp5p open state conformation is biologically relevant and that disruption of the interdomain interaction facilitates a large-scale conformational change of Prp5p during U2 snRNP-branch site recognition.


  • Organizational Affiliation

    State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing ATP-dependent RNA helicase PRP5493Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP5RNA5YBR237WYBR1603
EC: 3.6.4.13
UniProt
Find proteins for P21372 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21372 
Go to UniProtKB:  P21372
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21372
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.598α = 90
b = 86.598β = 90
c = 125.316γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references, Derived calculations