Crystal Structure of the Human Nudix Hydrolase Nudt16 in complex with FAD

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

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Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs.

Sharma, S.Grudzien-Nogalska, E.Hamilton, K.Jiao, X.Yang, J.Tong, L.Kiledjian, M.

(2020) Nucleic Acids Res 48: 6788-6798

  • DOI: https://doi.org/10.1093/nar/gkaa402
  • Primary Citation of Related Structures:  
    6X7U, 6X7V

  • PubMed Abstract: 

    We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5'caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins-Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U8 snoRNA-decapping enzymeA,
B [auth C]
184Homo sapiensMutation(s): 0 
Gene Names: NUDT16
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DE0 (Homo sapiens)
Explore Q96DE0 
Go to UniProtKB:  Q96DE0
GTEx:  ENSG00000198585 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96DE0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.721α = 90
b = 64.721β = 90
c = 77.751γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesR35GM118093

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Derived calculations, Refinement description