4TZ0

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

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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:  
    4TYN, 4TYW, 4TYY, 4TZ0, 4TZ6

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase MSS116, mitochondrialA509Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSS116, YDR194C, YD9346.05C
EC: 3.6.4.13
UniProt
Find proteins for P15424 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15424 
Go to UniProtKB:  P15424
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15424
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*AP*AP*AP*AP*AP*A)-3')B7Saccharomyces cerevisiae
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
BEF
Query on BEF
Download Ideal Coordinates CCD File 
D [auth A]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.979α = 90
b = 126.614β = 90
c = 55.553γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

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
  • Version 1.3: 2022-03-30
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy