2QT1

Human nicotinamide riboside kinase 1 in complex with nicotinamide riboside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    2P0E, 2QSY, 2QSZ, 2QT0, 2QT1

  • 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 adenylylation ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinamide riboside kinase 1A207Homo sapiensMutation(s): 0 
Gene Names: NRK1C9orf95NMRK1
EC: 2.7.1 (PDB Primary Data), 2.7.1.22 (UniProt), 2.7.1.173 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWW6 (Homo sapiens)
Explore Q9NWW6 
Go to UniProtKB:  Q9NWW6
PHAROS:  Q9NWW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWW6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.529α = 90
b = 141.906β = 90
c = 62.062γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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