6RCI | pdb_00006rci

Crystal structure of REXO2

• PDB DOI: https://doi.org/10.2210/pdb6RCI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-11 Released: 2019-10-09 
• Deposition Author(s): Spahr, H., Nicholls, T.J., Larsson, N.G., Gustafsson, C.M.
• Funding Organization(s): Max Planck Society, Swedish Research Council, Knut and Alice Wallenberg Foundation, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

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 76: 784-796.e6

• PubMed: 31588022 
• DOI: https://doi.org/10.1016/j.molcel.2019.09.010
• Primary Citation Related Structures: 
  6RCI, 6RCL, 6RCN


• 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 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.

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Organizational Affiliation: 
• Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden.
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 Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden.
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 Biophysics, Umeå University, Umeå 901 87, Sweden.
Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.
Research Core Unit Metabolomics, Hannover Medical School, 30625 Hannover, Germany.
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.
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. Electronic address: [e-mail].
Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.79 kDa 
• Atom Count: 2,910 
• Modeled Residue Count: 326 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoribonuclease, mitochondrial	A, B	180	Homo sapiens	Mutation(s): 0  Gene Names: REXO2, SFN, SMFN, CGI-114 EC: 3.1 (PDB Primary Data), 3.1.15 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3B8 (Homo sapiens) Explore Q9Y3B8  Go to UniProtKB:  Q9Y3B8
PHAROS:  Q9Y3B8 GTEx:  ENSG00000076043

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.164	α = 90
b = 128.492	β = 90
c = 170.22	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Spahr, H., Nicholls, T.J., Larsson, N.G., Gustafsson, C.M.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
Swedish Research Council	Sweden	--
Knut and Alice Wallenberg Foundation	Sweden	--
European Research Council		--

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Database references
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references