4QU4

Improved refinement of the Mtr4 apo crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

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
  • Primary Citation of Related Structures:  
    4QU4

  • 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 helicase core and a large arch domain that spans the core ...

    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 sean.johnson@usu.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DOB1A1108Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DOB1J1158MTR4MTR4/YJL050WYJL050W
EC: 3.6.4.13
UniProt
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47047 
Go to UniProtKB:  P47047
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47047
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.516α = 90
b = 133.516β = 90
c = 190.949γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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