6RCL

Crystal structure of REXO2-D199A-AA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.

Nicholls, T.J.Spahr, H.Jiang, S.Siira, S.J.Koolmeister, C.Sharma, S.Kauppila, J.H.K.Jiang, M.Kaever, V.Rackham, O.Chabes, A.Falkenberg, M.Filipovska, A.Larsson, N.G.Gustafsson, C.M.

(2019) Mol.Cell --: --

  • DOI: 10.1016/j.molcel.2019.09.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Oligoribonucleases are conserved enzymes that degrade short RNA molecules of up to 5 nt in length and are assumed to constitute the final stage of RNA turnover. Here we demonstrate that REXO2 is a specialized dinucleotide-degrading enzyme that shows ...

    Oligoribonucleases are conserved enzymes that degrade short RNA molecules of up to 5 nt in length and are assumed to constitute the final stage of RNA turnover. Here we demonstrate that REXO2 is a specialized dinucleotide-degrading enzyme that shows no preference between RNA and DNA dinucleotide substrates. A heart- and skeletal-muscle-specific knockout mouse displays elevated dinucleotide levels and alterations in gene expression patterns indicative of aberrant dinucleotide-primed transcription initiation. We find that dinucleotides act as potent stimulators of mitochondrial transcription initiation in vitro. Our data demonstrate that increased levels of dinucleotides can be used to initiate transcription, leading to an increase in transcription levels from both mitochondrial promoters and other, nonspecific sequence elements in mitochondrial DNA. Efficient RNA turnover by REXO2 is thus required to maintain promoter specificity and proper regulation of transcription in mammalian mitochondria.


    Organizational Affiliation

    Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.,Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden.,Research Core Unit Metabolomics, Hannover Medical School, 30625 Hannover, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden. Electronic address: nils-goran.larsson@ki.se.,Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, WA 6102, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia.,Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden.,Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden. Electronic address: claes.gustafsson@medkem.gu.se.,Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia.,Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligoribonuclease, mitochondrial
A, B
180Homo sapiensMutation(s): 0 
Gene Names: REXO2 (SFN, SMFN)
EC: 3.1.-.-
Find proteins for Q9Y3B8 (Homo sapiens)
Go to Gene View: REXO2
Go to UniProtKB:  Q9Y3B8
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*A)-3')C2synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 35.613α = 90.00
b = 125.835β = 90.00
c = 167.910γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
Swedish Research CouncilSweden--
Knut and Alice Wallenberg FoundationSweden--
European Research Council--

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection, Database references