2QT0

Human nicotinamide riboside kinase 1 in complex with nicotinamide riboside and an ATP analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nicotinamide Riboside Kinase Structures Reveal New Pathways to NAD(+).

Tempel, W.Rabeh, W.M.Bogan, K.L.Belenky, P.Wojcik, M.Seidle, H.F.Nedyalkova, L.Yang, T.Sauve, A.A.Park, H.W.Brenner, C.

(2007) Plos Biol. 5: e263-e263

  • DOI: 10.1371/journal.pbio.0050263
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The eukaryotic nicotinamide riboside kinase (Nrk) pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+) by phosphorylation and ade ...

    The eukaryotic nicotinamide riboside kinase (Nrk) pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+) by phosphorylation and adenylylation. Crystal structures of human Nrk1 bound to nucleoside and nucleotide substrates and products revealed an enzyme structurally similar to Rossmann fold metabolite kinases and allowed the identification of active site residues, which were shown to be essential for human Nrk1 and Nrk2 activity in vivo. Although the structures account for the 500-fold discrimination between nicotinamide riboside and pyrimidine nucleosides, no enzyme feature was identified to recognize the distinctive carboxamide group of nicotinamide riboside. Indeed, nicotinic acid riboside is a specific substrate of human Nrk enzymes and is utilized in yeast in a novel biosynthetic pathway that depends on Nrk and NAD+ synthetase. Additionally, nicotinic acid riboside is utilized in vivo by Urh1, Pnp1, and Preiss-Handler salvage. Thus, crystal structures of Nrk1 led to the identification of new pathways to NAD+.


    Organizational Affiliation

    Structural Genomics Consortium and Department of Pharmacology, University of Toronto, Toronto, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide riboside kinase 1
A
207Homo sapiensMutation(s): 0 
Gene Names: NMRK1 (C9orf95, NRK1)
EC: 2.7.1.22
Find proteins for Q9NWW6 (Homo sapiens)
Go to Gene View: NMRK1
Go to UniProtKB:  Q9NWW6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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

Download SDF File 
Download CCD File 
A
Nicotinamide riboside
3-(aminocarbonyl)-1-beta-D-ribofuranosylpyridinium
C11 H15 N2 O5
JLEBZPBDRKPWTD-TURQNECASA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.025α = 90.00
b = 97.025β = 90.00
c = 44.801γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description