3K44

Crystal Structure of Drosophila melanogaster Pur-alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

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This is version 1.1 of the entry. See complete history


Literature

X-ray structure of Pur-alpha reveals a Whirly-like fold and an unusual nucleic-acid binding surface

Graebsch, A.Roche, S.Niessing, D.

(2009) Proc Natl Acad Sci U S A 106: 18521-18526

  • DOI: 10.1073/pnas.0907990106
  • Primary Citation of Related Structures:  
    3K44

  • PubMed Abstract: 
  • The PUR protein family is a distinct and highly conserved class that is characterized by its sequence-specific RNA- and DNA-binding. Its best-studied family member, Pur-alpha, acts as a transcriptional regulator, as host factor for viral replication, and as cofactor for mRNP localization in dendrites ...

    The PUR protein family is a distinct and highly conserved class that is characterized by its sequence-specific RNA- and DNA-binding. Its best-studied family member, Pur-alpha, acts as a transcriptional regulator, as host factor for viral replication, and as cofactor for mRNP localization in dendrites. Pur-alpha-deficient mice show severe neurologic defects and die after birth. Nucleic-acid binding by Pur-alpha is mediated by its central core region, for which no structural information is available. We determined the x-ray structure of residues 40 to 185 from Drosophila melanogaster Pur-alpha, which constitutes a major part of the core region. We found that this region contains two almost identical structural motifs, termed "PUR repeats," which interact with each other to form a PUR domain. DNA- and RNA-binding studies confirmed that PUR domains are indeed functional nucleic-acid binding domains. Database analysis show that PUR domains share a fold with the Whirly class of nucleic-acid binding proteins. Structural analysis combined with mutational studies suggest that a PUR domain binds nucleic acids through two independent surface regions involving concave beta-sheets. Structure-based sequence alignment revealed that the core region harbors a third PUR repeat at its C terminus. Subsequent characterization by small-angle x-ray scattering (SAXS) and size-exclusion chromatography indicated that PUR repeat III mediates dimerization of Pur-alpha. Surface envelopes calculated from SAXS data show that the Pur-alpha dimer consisting of repeats I to III is arranged in a Z-like shape. This unexpected domain organization of the entire core domain of Pur-alpha has direct implications for ssDNA/ssRNA and dsDNA binding.


    Organizational Affiliation

    Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchionini-Strasse 25, Munich 81377, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine-rich binding protein-alpha, isoform BA, B, C, D146Drosophila melanogasterMutation(s): 0 
Gene Names: CG1507Dmel_CG1507pur-alphaPur-alphaDmel\CG1507dPur alphaPur alphaPur-apurAPURalpha
UniProt
Find proteins for Q95RR6 (Drosophila melanogaster)
Explore Q95RR6 
Go to UniProtKB:  Q95RR6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.168α = 90
b = 62.544β = 90.01
c = 64.479γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
CRUNCH2model building
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CRUNCH2phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance