2QL6

human nicotinamide riboside kinase (NRK1)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of human nicotinamide riboside kinase

Khan, J.A., Xiang, S., Tong, L.

(2007) Structure 15: 1005-1013

  • DOI: 10.1016/j.str.2007.06.017
  • Primary Citation of Related Structures:  
    2QG6, 2QL6

  • PubMed Abstract: 

    • Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD(+) as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low ...

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD(+) as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 A resolution and in a ternary complex with ADP and tiazofurin at 2.7 A resolution. The active site is located in a groove between the central parallel beta sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations.

    Organizational Affiliation: 

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
nicotinamide riboside kinase 1
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
199Homo sapiensMutation(s): 0 
Gene Names: NRK1, C9orf95, NMRK1
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
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
IA [auth J],
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
IA [auth J],
KA [auth K],
MA [auth L],
OA [auth M],
Q [auth A],
QA [auth N],
S [auth B],
SA [auth O],
U [auth C],
UA [auth P],
W [auth D],
Y [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
TIZ
Query on TIZ
Download Ideal Coordinates CCD File 
BA [auth F],
DA [auth G],
FA [auth H],
HA [auth I],
JA [auth J],
BA [auth F],
DA [auth G],
FA [auth H],
HA [auth I],
JA [auth J],
LA [auth K],
NA [auth L],
PA [auth M],
R [auth A],
RA [auth N],
T [auth B],
TA [auth O],
V [auth C],
VA [auth P],
X [auth D],
Z [auth E]
(1R)-1-[4-(AMINOCARBONYL)-1,3-THIAZOL-2-YL]-1,4-ANHYDRO-D-RIBITOL
C9 H12 N2 O5 S
FVRDYQYEVDDKCR-DBRKOABJSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.71α = 90
b = 99.96β = 91.57
c = 145.59γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description