2XSQ

Crystal structure of human Nudix motif 16 (NUDT16) in complex with IMP and magnesium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Specificity of Human Nudt16 and its Regulation by Inosine Monophosphate.

Tresaugues, L.Lundback, T.Welin, M.Flodin, S.Nyman, T.Silvander, C.Graslund, S.Nordlund, P.

(2015) PLoS One 10: 31507

  • DOI: 10.1371/journal.pone.0131507
  • Primary Citation of Related Structures:  
    2XSQ

  • PubMed Abstract: 
  • Human NUDT16 is a member of the NUDIX hydrolase superfamily. After having been initially described as an mRNA decapping enzyme, recent studies conferred it a role as an "housecleaning" enzyme specialized in the removal of hazardous (deoxy)inosine dip ...

    Human NUDT16 is a member of the NUDIX hydrolase superfamily. After having been initially described as an mRNA decapping enzyme, recent studies conferred it a role as an "housecleaning" enzyme specialized in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. Here we present the crystal structure of human NUDT16 both in its apo-form and in complex with its product inosine monophosphate (IMP). NUDT16 appears as a dimer whose formation generates a positively charged trench to accommodate substrate-binding. Complementation of the structural data with detailed enzymatic and biophysical studies revealed the determinants of substrate recognition and particularly the importance of the substituents in position 2 and 6 on the purine ring. The affinity for the IMP product, harboring a carbonyl in position 6 on the base, compared to purine monophosphates lacking a H-bond acceptor in this position, implies a catalytic cycle whose rate is primarily regulated by the product-release step. Finally, we have also characterized a phenomenon of inhibition by the product of the reaction, IMP, which might exclude non-deleterious nucleotides from NUDT16-mediated hydrolysis regardless of their cellular concentration. Taken together, this study details structural and regulatory mechanisms explaining how substrates are selected for hydrolysis by human NUDT16.


    Organizational Affiliation

    Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U8 SNORNA-DECAPPING ENZYMEA217Homo sapiensMutation(s): 0 
Gene Names: NUDT16
EC: 3.6.1 (PDB Primary Data), 3.6.1.62 (UniProt), 3.6.1.64 (UniProt)
Find proteins for Q96DE0 (Homo sapiens)
Explore Q96DE0 
Go to UniProtKB:  Q96DE0
NIH Common Fund Data Resources
PHAROS  Q96DE0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download CCD File 
A
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.583α = 90
b = 141.583β = 90
c = 141.583γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references, Version format compliance
  • Version 1.2: 2017-12-13
    Changes: Structure summary