6SCX

Crystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Decapping Enzyme NUDT12 Partners with BLMH for Cytoplasmic Surveillance of NAD-Capped RNAs.

Wu, H.Li, L.Chen, K.M.Homolka, D.Gos, P.Fleury-Olela, F.McCarthy, A.A.Pillai, R.S.

(2019) Cell Rep 29: 4422-4434.e13

  • DOI: 10.1016/j.celrep.2019.11.108

  • PubMed Abstract: 
  • RNA polymerase II transcripts receive a protective 5',5'-triphosphate-linked 7-methylguanosine (m <sup>7 </sup>G) cap, and its removal by decapping enzymes like DCP2 is critical for initiation of RNA decay. Alternative RNA caps can be acquired when t ...

    RNA polymerase II transcripts receive a protective 5',5'-triphosphate-linked 7-methylguanosine (m 7 G) cap, and its removal by decapping enzymes like DCP2 is critical for initiation of RNA decay. Alternative RNA caps can be acquired when transcription initiation uses metabolites like nicotinamide adenine dinucleotide (NAD), generating NAD-RNAs. Here, we identify human NUDT12 as a cytosolic NAD-RNA decapping enzyme. NUDT12 is active only as homodimers, with each monomer contributing to creation of the two functional catalytic pockets. We identify an ∼600-kDa dodecamer complex between bleomycin hydrolase (BLMH) and NUDT12, with BLMH being required for localization of NUDT12 to a few discrete cytoplasmic granules that are distinct from P-bodies. Both proteins downregulate gene expression when artificially tethered to a reporter RNA in vivo. Furthermore, loss of Nudt12 results in a significant upregulation of circadian clock transcripts in mouse liver. Overall, our study points to a physiological role for NUDT12 in the cytosolic surveillance of NAD-RNAs.


    Organizational Affiliation

    Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.,Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland. Electronic address: ramesh.pillai@unige.ch.,European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisomal NADH pyrophosphatase NUDT12
A, B, C
352Homo sapiensMutation(s): 0 
Gene Names: NUDT12
EC: 3.6.1.22
Find proteins for Q9BQG2 (Homo sapiens)
Go to Gene View: NUDT12
Go to UniProtKB:  Q9BQG2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGP
Query on MGP

Download SDF File 
Download CCD File 
A, B, C
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
C11 H19 N5 O14 P3
DKVRNHPCAOHRSI-KQYNXXCUSA-O
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B, C
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.232 
  • Space Group: H 3 2
  • Diffraction Data DOI: 
    10.15785/SBGRID/716 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 229.859α = 90.00
b = 229.859β = 90.00
c = 159.012γ = 120.00
Software Package:
Software NamePurpose
pointlessdata scaling
STARANISOdata scaling
PDB_EXTRACTdata extraction
AutoPROCdata scaling
BUSTERrefinement
Cootmodel building
PHASERphasing
XDSdata reduction
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release