1U0R

Crystal structure of Mycobacterium tuberculosis NAD kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel fold revealed by Mycobacterium tuberculosis NAD kinase, a key allosteric enzyme in NADP biosynthesis

Garavaglia, S.Raffaelli, N.Finaurini, L.Magni, G.Rizzi, M.

(2004) J.Biol.Chem. 279: 40980-40986

  • DOI: 10.1074/jbc.M406586200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NAD kinase catalyzes the magnesium-dependent phosphorylation of NAD, representing the sole source of freshly synthesized NADP in all organisms. The enzyme is essential for the growth of the deadly multidrug-resistant pathogen Mycobacterium tuberculos ...

    NAD kinase catalyzes the magnesium-dependent phosphorylation of NAD, representing the sole source of freshly synthesized NADP in all organisms. The enzyme is essential for the growth of the deadly multidrug-resistant pathogen Mycobacterium tuberculosis and is an attractive target for novel antitubercular agents. The crystal structure of NAD kinase has been solved by multiwavelength anomalous dispersion at a resolution of 2.3 A in its T state. Two crystal forms have been obtained revealing either a dimer or a tetramer. The enzyme architecture discloses a novel molecular arrangement, with each subunit consisting of an alpha/beta N-terminal domain and a C-terminal 12-stranded beta sandwich domain, connected by swapped beta strands. The C-terminal domain shows a striking internal approximate 222 symmetry and an unprecedented topology, revealing a novel fold within the family of all beta structures. The catalytic site is located in the long crevice that defines the interface between the domains. The conserved GGDG structural fingerprint of the catalytic site is reminiscent of the related region in 6-phosphofructokinase, supporting the hypothesis that NAD kinase belongs to a newly reported superfamily of kinases.


    Related Citations: 
    • Characterization of Mycobacterium tuberculosis NAD kinase: functional analysis of the full-length enzyme by site-directed mutagenesis
      Raffaelli, N.,Finaurini, L.,Mazzola, F.,Pucci, L.,Sorci, L.,Amici, A.,Magni, G.
      (2004) Biochemistry 43: 7610


    Organizational Affiliation

    Dipartimento di Scienze Chimiche, Alimentari, Farmaceutiche, Farmacologiche-Istituto Nazionale Fisica della Materia, University of Piemonte Orientale "Amedeo Avogadro," Via Bovio 6, 28100 Novara, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inorganic polyphosphate/ATP-NAD kinase
A, B, C, D
307Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ppnK
EC: 2.7.1.23
Find proteins for P9WHV7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHV7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.223 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 118.510α = 90.00
b = 118.510β = 90.00
c = 222.300γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SHELXSphasing
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance