3DLA

X-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium tuberculosis bound to NaAD+ and DON

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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Literature

Regulation of active site coupling in glutamine-dependent NAD(+) synthetase.

LaRonde-LeBlanc, N., Resto, M., Gerratana, B.

(2009) Nat Struct Mol Biol 16: 421-429

  • DOI: https://doi.org/10.1038/nsmb.1567
  • Primary Citation of Related Structures:  
    3DLA

  • PubMed Abstract: 

    NAD(+) is an essential metabolite both as a cofactor in energy metabolism and redox homeostasis and as a regulator of cellular processes. In contrast to humans, Mycobacterium tuberculosis NAD(+) biosynthesis is absolutely dependent on the activity of a multifunctional glutamine-dependent NAD(+) synthetase, which catalyzes the ATP-dependent formation of NAD(+) at the synthetase domain using ammonia derived from L-glutamine in the glutaminase domain. Here we report the kinetics and structural characterization of M. tuberculosis NAD(+) synthetase. The kinetics data strongly suggest tightly coupled regulation of the catalytic activities. The structure, the first of a glutamine-dependent NAD(+) synthetase, reveals a homooctameric subunit organization suggesting a tight dependence of catalysis on the quaternary structure, a 40-A intersubunit ammonia tunnel and structural elements that may be involved in the transfer of information between catalytic sites.

    • Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742-2021, USA. nlaronde@umd.edu


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine-dependent NAD(+) synthetase
A, B, C, D
680Mycobacterium tuberculosisMutation(s): 0 
Gene Names: nadE, Rv2438c, MT2513, MTCY428.08
EC: 6.3.5.1
UniProt
Find proteins for P9WJJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJJ3 
Go to UniProtKB:  P9WJJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJJ3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DND
Query on DND
Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
Q [auth C],
V [auth D]		NICOTINIC ACID ADENINE DINUCLEOTIDE
C21 H27 N6 O15 P2
SENPVEZBRZQVST-HISDBWNOSA-O
ONL
Query on ONL
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]		5-OXO-L-NORLEUCINE
C6 H11 N O3
KSIJECNNZVKMJG-YFKPBYRVSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth D]
J [auth A]
K [auth A]
M [auth B]
N [auth B]
AA [auth D],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NXX PDBBind:  3DLA Kd: 3.50e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.13α = 90
b = 178.13β = 90
c = 215.177γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 2.0: 2019-10-23
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary