4J7M

Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing.

Jiao, X.Chang, J.H.Kilic, T.Tong, L.Kiledjian, M.

(2013) Mol.Cell 50: 104-115

  • DOI: 10.1016/j.molcel.2013.02.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recently, we reported that two homologous yeast proteins, Rai1 and Dxo1, function in a quality control mechanism to clear cells of incompletely 5' end-capped messenger RNAs (mRNAs). Here, we report that their mammalian homolog, Dom3Z (referred to as ...

    Recently, we reported that two homologous yeast proteins, Rai1 and Dxo1, function in a quality control mechanism to clear cells of incompletely 5' end-capped messenger RNAs (mRNAs). Here, we report that their mammalian homolog, Dom3Z (referred to as DXO), possesses pyrophosphohydrolase, decapping, and 5'-to-3' exoribonuclease activities. Surprisingly, we found that DXO preferentially degrades defectively capped pre-mRNAs in cells. Additional studies show that incompletely capped pre-mRNAs are inefficiently spliced at all introns, a fact that contrasts with current understanding, and are also poorly cleaved for polyadenylation. Crystal structures of DXO in complex with substrate mimic and products at a resolution of up to 1.5Å provide elegant insights into the catalytic mechanism and molecular basis for their three apparently distinct activities. Our data reveal a pre-mRNA 5' end capping quality control mechanism in mammalian cells, indicating DXO as the central player for this mechanism, and demonstrate an unexpected intimate link between proper 5' end capping and subsequent pre-mRNA processing.


    Organizational Affiliation

    Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein Dom3Z
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
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*(U37)P*(U37)P*UP*U)-3')B5synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UBD
Query on UBD

Download SDF File 
Download CCD File 
A
URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE)
C9 H14 N2 O12 P2
ZPVPRWPOZBXDKD-XVFCMESISA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
U37
Query on U37
B
RNA LINKINGC9 H13 N2 O8 P SU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.985α = 90.00
b = 87.837β = 111.69
c = 54.356γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-02-13 
  • Released Date: 2013-03-27 
  • Deposition Author(s): Chang, J.H., Tong, L.

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references