6O3P

Crystal structure of the catalytic domain of mouse Nudt12 in complex with AMP and 3 Mg2+ ions

  • Classification: HYDROLASE
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2019-02-27 Released: 2019-05-29 
  • Deposition Author(s): Tong, L., Wu, Y.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and mechanistic basis of mammalian Nudt12 RNA deNADding.

Grudzien-Nogalska, E.Wu, Y.Jiao, X.Cui, H.Mateyak, M.K.Hart, R.P.Tong, L.Kiledjian, M.

(2019) Nat.Chem.Biol. 15: 575-582

  • DOI: 10.1038/s41589-019-0293-7

  • PubMed Abstract: 
  • We recently demonstrated that mammalian cells harbor nicotinamide adenine dinucleotide (NAD)-capped messenger RNAs that are hydrolyzed by the DXO deNADding enzyme. Here, we report that the Nudix protein Nudt12 is a second mammalian deNADding enzyme s ...

    We recently demonstrated that mammalian cells harbor nicotinamide adenine dinucleotide (NAD)-capped messenger RNAs that are hydrolyzed by the DXO deNADding enzyme. Here, we report that the Nudix protein Nudt12 is a second mammalian deNADding enzyme structurally and mechanistically distinct from DXO and targeting different RNAs. The crystal structure of mouse Nudt12 in complex with the deNADding product AMP and three Mg 2+ ions at 1.6 Å resolution provides insights into the molecular basis of the deNADding activity in the NAD pyrophosphate. Disruption of the Nudt12 gene stabilizes transfected NAD-capped RNA in cells, and its endogenous NAD-capped mRNA targets are enriched in those encoding proteins involved in cellular energetics. Furthermore, exposure of cells to nutrient or environmental stress manifests changes in NAD-capped RNA levels that are selectively responsive to Nudt12 or DXO, respectively, indicating an association of deNADding to cellular metabolism.


    Organizational Affiliation

    Department Biological Sciences, Columbia University, New York, NY, USA. ltong@columbia.edu.,Department Biological Sciences, Columbia University, New York, NY, USA.,Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA. kiledjian@biology.rutgers.edu.,Department Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisomal NADH pyrophosphatase NUDT12
A, B
339Mus musculusMutation(s): 3 
Gene Names: Nudt12
EC: 3.6.1.22
Find proteins for Q9DCN1 (Mus musculus)
Go to UniProtKB:  Q9DCN1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 56.207α = 102.40
b = 58.550β = 115.19
c = 61.707γ = 104.66
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-02-27 
  • Released Date: 2019-05-29 
  • Deposition Author(s): Tong, L., Wu, Y.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited States--

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release