6AIX

Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Molecular mechanism for the inhibition of DXO by adenosine 3',5'-bisphosphate.

Yun, J.S.Yoon, J.H.Choi, Y.J.Son, Y.J.Kim, S.Tong, L.Chang, J.H.

(2018) Biochem. Biophys. Res. Commun. 504: 89-95

  • DOI: 10.1016/j.bbrc.2018.08.135
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The decapping exoribonuclease DXO functions in pre-mRNA capping quality control, and shows multiple biochemical activities such as decapping, deNADding, pyrophosphohydrolase, and 5'-3' exoribonuclease activities. Previous studies revealed the molecul ...

    The decapping exoribonuclease DXO functions in pre-mRNA capping quality control, and shows multiple biochemical activities such as decapping, deNADding, pyrophosphohydrolase, and 5'-3' exoribonuclease activities. Previous studies revealed the molecular mechanisms of DXO based on the structures in complexes with a product, substrate mimic, cap analogue, and 3'-NADP + . Despite several reports on the substrate-specific reaction mechanism, the inhibitory mechanism of DXO remains elusive. Here, we demonstrate that adenosine 3', 5'-bisphosphate (pAp), a known inhibitor of the 5'-3' exoribonuclease Xrn1, inhibits the nuclease activity of DXO based on the results of structural and biochemical experiments. We determined the crystal structure of the DXO-pAp-Mg 2+ complex at 1.8 Å resolution. In comparison with the DXO-RNA product complex, the position of pAp is well superimposed with the first nucleotide of the product RNA in the vicinity of two magnesium ions. Furthermore, biochemical assays showed that the inhibition by pAp is comparable between Xrn1 and DXO. Collectively, these structural and biochemical studies reveal that pAp inhibits the activities of DXO by occupying the active site to act as a competitive inhibitor.


    Organizational Affiliation

    Department of Biology Education, Kyungpook National University, Daegu 41566, South Korea.,Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA.,New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Electronic address: ltong@columbia.edu.,Department of Biology Education, Kyungpook National University, Daegu 41566, South Korea; Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Electronic address: jhcbio@knu.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Decapping and exoribonuclease protein
A
378Mus musculusMutation(s): 0 
Gene Names: Dxo (Dom3z, Ng6)
EC: 3.1.13.-, 3.6.1.-
Find proteins for O70348 (Mus musculus)
Go to UniProtKB:  O70348
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A3P
Query on A3P

Download SDF File 
Download CCD File 
A
ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.460α = 90.00
b = 87.872β = 114.32
c = 50.097γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-25 
  • Released Date: 2018-10-17 
  • Deposition Author(s): Chang, J.H., Tong, L.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2016R1C1B2009691
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118093

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release