1KQP

NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.106 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.

Symersky, J.Devedjiev, Y.Moore, K.Brouillette, C.DeLucas, L.

(2002) Acta Crystallogr.,Sect.D 58: 1138-1146


  • PubMed Abstract: 
  • The final step of NAD+ biosynthesis includes an amide transfer to nicotinic acid adenine dinucleotide (NaAD) catalyzed by NAD+ synthetase. This enzyme was co-crystallized in microgravity with natural substrates NaAD and ATP at pH 8.5. The crystal was ...

    The final step of NAD+ biosynthesis includes an amide transfer to nicotinic acid adenine dinucleotide (NaAD) catalyzed by NAD+ synthetase. This enzyme was co-crystallized in microgravity with natural substrates NaAD and ATP at pH 8.5. The crystal was exposed to ammonium ions, synchrotron diffraction data were collected and the atomic model was refined anisotropically at 1 A resolution to R = 11.63%. Both binding sites are occupied by the NAD-adenylate intermediate, pyrophosphate and two magnesium ions. The atomic resolution of the structure allows better definition of non-planar peptide groups, reveals a low mean anisotropy of protein and substrate atoms and indicates the H-atom positions of the phosphoester group of the reaction intermediate. The phosphoester group is protonated at the carbonyl O atom O7N, suggesting a carbenium-ion structure stabilized by interactions with two solvent sites presumably occupied by ammonia and a water molecule. A mechanism is proposed for the second catalytic step, which includes a nucleophilic attack by the ammonia molecule on the intermediate.


    Related Citations: 
    • Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis
      Devedjiev, Y.,Symersky, J.,Singh, R.,Jedrzejas, M.,Brouillette, C.,Brouillette, W.,Muccio, D.,Chattopadhyay, D.,DeLucas, L.
      (2001) Acta Crystallogr.,Sect.D 57: 806
    • A novel deamido-NAD+ binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure
      Rizzi, M.,Bolognesi, M.,Coda, A.
      (1998) Structure 6: 1129
    • Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis
      Rizzi, M.,Nessi, C.,Mattevi, A.,Coda, A.,Bolognesi, M.,Galizzi, A.
      (1996) Embo J. 15: 5125


    Organizational Affiliation

    Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NH(3)-dependent NAD(+) synthetase
A, B
271Bacillus subtilis (strain 168)Gene Names: nadE (outB)
EC: 6.3.1.5
Find proteins for P08164 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P08164
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A, B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
ADJ
Query on ADJ

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Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE-ADENYLATE INTERMEDIATE
NADP-A
C31 H44 N11 O21 P3
DBSVVYFUZBLHSN-JFLYKPBPSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.106 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.280α = 90.00
b = 84.790β = 110.50
c = 59.640γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-28
    Type: Initial release
  • Version 1.1: 2007-10-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-08-03
    Type: Atomic model