Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 126.58 kDa 
• Atom Count: 6680 
• Modelled Residue Count: 942 
• Deposited Residue Count: 1108 
• Unique protein chains: 1

4QU4

Improved refinement of the Mtr4 apo crystal structure

• PDB DOI: 10.2210/pdb4QU4/pdb
• Entry: 4QU4 supersedes: 3L9O

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-10 Released: 2014-12-03 
• Deposition Author(s): Johnson, S.J., Taylor, L.L.

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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 

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

• PubMed: 25414331 
• 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. 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.

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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

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DOB1	A	1108	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: DOB1, J1158, MTR4, MTR4/YJL050W, YJL050W EC: 3.6.4.13
UniProt
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47047  Go to UniProtKB:  P47047

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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 = 133.516	α = 90
b = 133.516	β = 90
c = 190.949	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-10 
• Released Date: 2014-12-03 
Deposition Author(s): Johnson, S.J., Taylor, L.L.
• This entry supersedes: 3L9O

Revision History  

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