4QU4

Improved refinement of the Mtr4 apo crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.392 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding.

Taylor, L.L.Jackson, R.N.Rexhepaj, M.King, A.K.Lott, L.K.van Hoof, A.Johnson, S.J.

(2014) Nucleic Acids Res. 42: 13861-13872

  • DOI: 10.1093/nar/gku1208

  • PubMed Abstract: 
  • Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3'-5' turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like ...

    Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3'-5' turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The 'ratchet helix' is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues along the ratchet helix alters in vitro activity in Mtr4 and TRAMP and causes slow growth phenotypes in vivo. We also identify a residue on the ratchet helix that influences Mtr4 affinity for polyadenylated substrates. Previous work indicated that deletion of the arch domain has minimal effect on Mtr4 unwinding activity. We now show that combining the arch deletion with ratchet helix mutations abolishes helicase activity and produces a lethal in vivo phenotype. These studies demonstrate that the ratchet helix modulates helicase activity and suggest that the arch domain plays a previously unrecognized role in unwinding substrates.


    Related Citations: 
    • The crystal structure of MTR4 reveals a novel arch domain required for rRNA processing.
      Jackson, R.N.,Klauer, A.A.,Hintze, B.J.,Robinson, H.,van Hoof, A.,Johnson, S.J.
      (2010) Embo J. 29: 2205


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.,Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA.,Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA sean.johnson@usu.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase DOB1
A
1108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MTR4 (DOB1)
EC: 3.6.4.13
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47047
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.392 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 133.516α = 90.00
b = 133.516β = 90.00
c = 190.949γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction
SOLVEphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references