6J7Z

Human mitochondrial Oligoribonuclease in complex with RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.005 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into nanoRNA degradation by human Rexo2.

Chu, L.Y.Agrawal, S.Chen, Y.P.Yang, W.Z.Yuan, H.S.

(2019) Rna 25: 737-746

  • DOI: 10.1261/rna.070557.119
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human RNA exoribonuclease 2 (Rexo2) is an evolutionarily conserved 3'-to-5' DEDDh-family exonuclease located primarily in mitochondria. Rexo2 degrades small RNA oligonucleotides of <5 nucleotides (nanoRNA) in a way similar to <i>Escherichia coli </i ...

    Human RNA exoribonuclease 2 (Rexo2) is an evolutionarily conserved 3'-to-5' DEDDh-family exonuclease located primarily in mitochondria. Rexo2 degrades small RNA oligonucleotides of <5 nucleotides (nanoRNA) in a way similar to Escherichia coli Oligoribonuclease (ORN), suggesting that it plays a role in RNA turnover in mitochondria. However, how Rexo2 preferentially binds and degrades nanoRNA remains elusive. Here, we show that Rexo2 binds small RNA and DNA oligonucleotides with the highest affinity, and it is most robust in degrading small nanoRNA into mononucleotides in the presence of magnesium ions. We further determined three crystal structures of Rexo2 in complex with single-stranded RNA or DNA at resolutions of 1.8-2.2 Å. Rexo2 forms a homodimer and interacts mainly with the last two 3'-end nucleobases of substrates by hydrophobic and π-π stacking interactions via Leu53, Trp96, and Tyr164, signifying its preference in binding and degrading short oligonucleotides without sequence specificity. Crystal structure of Rexo2 is highly similar to that of the RNA-degrading enzyme ORN, revealing a two-magnesium-ion-dependent hydrolysis mechanism. This study thus provides the molecular basis for human Rexo2, showing how it binds and degrades nanoRNA into nucleoside monophosphates and plays a crucial role in RNA salvage pathways in mammalian mitochondria.


    Organizational Affiliation

    Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 11490, Republic of China.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu, Taiwan 30013, Republic of China.,Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligoribonuclease, mitochondrial
A, B
186Homo sapiensMutation(s): 1 
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*UP*U)-3')C2synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.005 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 86.192α = 90.00
b = 125.892β = 90.00
c = 86.008γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release