4TYW

DEAD-box helicase Mss116 bound to ssRNA and ADP-BeF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.

Mallam, A.L.Sidote, D.J.Lambowitz, A.M.

(2014) Elife 3: e04630-e04630

  • DOI: 10.7554/eLife.04630
  • Primary Citation of Related Structures:  
    4TZ6, 4TYW, 4TYN, 4TZ0, 4TYY

  • PubMed Abstract: 
  • How different helicase families with a conserved catalytic 'helicase core' evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. In this study, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism ...

    How different helicase families with a conserved catalytic 'helicase core' evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. In this study, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the 'closed-state' helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions.


    Organizational Affiliation

    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase MSS116, mitochondrialA509Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSS116YDR194CYD9346.05C
EC: 3.6.4.13
UniProt
Find proteins for P15424 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15424 
Go to UniProtKB:  P15424
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')B7Saccharomyces cerevisiae
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP (Subject of Investigation/LOI)
    Query on ADP

    Download Ideal Coordinates CCD File 
    F [auth A]ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    BEF
    Query on BEF

    Download Ideal Coordinates CCD File 
    E [auth A]BERYLLIUM TRIFLUORIDE ION
    Be F3
    OGIAHMCCNXDTIE-UHFFFAOYSA-K
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.254 
    • R-Value Work: 0.216 
    • R-Value Observed: 0.218 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 89.829α = 90
    b = 126.26β = 90
    c = 55.545γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-12-31
      Type: Initial release
    • Version 1.1: 2015-01-21
      Changes: Database references
    • Version 1.2: 2015-03-04
      Changes: Database references