6WRE

Crystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report



Literature

A novel 5'-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes.

Doamekpor, S.K.Gozdek, A.Kwasnik, A.Kufel, J.Tong, L.

(2020) Nucleic Acids Res 48: 349-358

  • DOI: 10.1093/nar/gkz1107
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Modifications at the 5'-end of RNAs play a pivotal role in determining their fate. In eukaryotes, the DXO/Rai1 family of enzymes removes numerous 5'-end RNA modifications, thereby regulating RNA turnover. Mouse DXO catalyzes the elimination of incomp ...

    Modifications at the 5'-end of RNAs play a pivotal role in determining their fate. In eukaryotes, the DXO/Rai1 family of enzymes removes numerous 5'-end RNA modifications, thereby regulating RNA turnover. Mouse DXO catalyzes the elimination of incomplete 5'-end caps (including pyrophosphate) and the non-canonical NAD+ cap on mRNAs, and possesses distributive 5'-3' exoribonuclease activity toward 5'-monophosphate (5'-PO4) RNA. Here, we demonstrate that DXO also catalyzes the hydrolysis of RNAs bearing a 5'-hydroxyl group (5'-OH RNA). The crystal structure of DXO in complex with a 5'-OH RNA substrate mimic at 2.0 Å resolution provides elegant insight into the molecular mechanism of this activity. More importantly, the structure predicts that DXO first removes a dinucleotide from 5'-OH RNA. Our nuclease assays confirm this prediction and demonstrate that this 5'-hydroxyl dinucleotide hydrolase (HDH) activity for DXO is higher than the subsequent 5'-3' exoribonuclease activity for selected substrates. Fission yeast Rai1 also has HDH activity although it does not have 5'-3' exonuclease activity, and the Rat1-Rai1 complex can completely degrade 5'-OH RNA. An Arabidopsis DXO1 variant is active toward 5'-OH RNA but prefers 5'-PO4 RNA. Collectively, these studies demonstrate the diverse activities of DXO/Rai1 and expands the collection of RNA substrates that can undergo 5'-3' mediated decay.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Decapping and exoribonuclease protein
A
378Mus musculusMutation(s): 0 
Gene Names: DxoDom3zNg6
EC: 3.1.13 (PDB Primary Data), 3.6.1 (PDB Primary Data)
Find proteins for O70348 (Mus musculus)
Go to UniProtKB:  O70348
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*(U37)P*(U37)P*UP)-3')D6Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U3P
Query on U3P

Download CCD File 
A
3'-URIDINEMONOPHOSPHATE
C9 H13 N2 O9 P
FOGRQMPFHUHIGU-XVFCMESISA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.182α = 90
b = 87.795β = 112.35
c = 53.88γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118093

Revision History 

  • Version 1.0: 2020-05-13
    Type: Initial release