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


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
  • Structures With Same Primary Citation

  • 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 1A207Homo sapiensMutation(s): 0 
Gene Names: NRK1C9orf95NMRK1
EC: 2.7.1 (PDB Primary Data), 2.7.1.22 (UniProt), 2.7.1.173 (UniProt)
Find proteins for Q9NWW6 (Homo sapiens)
Explore Q9NWW6 
Go to UniProtKB:  Q9NWW6
NIH Common Fund Data Resources
PHAROS  Q9NWW6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NNR
Query on NNR

Download CCD File 
A
Nicotinamide riboside
C11 H15 N2 O5
JLEBZPBDRKPWTD-TURQNECASA-O
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
A
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-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



Entry History 

Deposition Data

Revision History 

  • 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