4TYW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.197 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


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:  

  • 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 locall ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase MSS116, mitochondrial
A
509Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MSS116
EC: 3.6.4.13
Find proteins for P15424 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P15424
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')B7Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.197 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 89.829α = 90.00
b = 126.260β = 90.00
c = 55.545γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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