6F3H

Crystal structure of Dss1 exoribonuclease active site mutant D477N from Candida glabrata


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.703 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components.

Razew, M.Warkocki, Z.Taube, M.Kolondra, A.Czarnocki-Cieciura, M.Nowak, E.Labedzka-Dmoch, K.Kawinska, A.Piatkowski, J.Golik, P.Kozak, M.Dziembowski, A.Nowotny, M.

(2018) Nat Commun 9: 97-97

  • DOI: 10.1038/s41467-017-02570-5
  • Primary Citation of Related Structures:  6F4A

  • PubMed Abstract: 
  • Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mt ...

    Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase-exoribonuclease coordination. mtEXO is composed of Dss1 3'-to-5' exoribonuclease and Suv3 helicase. It is the master regulator of mitochondrial gene expression in yeast. Here, we present the structure of mtEXO and a description of its mechanism of action. The crystal structure of Dss1 reveals domains that are responsible for interactions with Suv3. Importantly, these interactions are compatible with the conformational changes of Suv3 domains during the helicase cycle. We demonstrate that mtEXO is an intimate complex which forms an RNA-binding channel spanning its entire structure, with Suv3 helicase feeding the 3' end of the RNA toward the active site of Dss1.


    Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exoribonuclease II, mitochondrial
A, B
832N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')C6Escherichia coli BL21(DE3)
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*AP*CP*UP*GP*A)-3')D6Escherichia coli BL21(DE3)
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.703 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 73.370α = 106.21
b = 83.230β = 106.56
c = 110.370γ = 90.93
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Science Center PolandPoland00463

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release