2NSY

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS IN COMPLEX WITH NAD-ADENYLATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 1129-1140


  • PubMed Abstract: 
  • Nicotinamide adenine dinucleotide (NAD+) has a central role in life processes. The ubiquitous enzyme NAD+ synthetase catalyzes a key step in NAD+ biosynthesis, transforming deamido-NAD+ into NAD+ by a two-step reaction. NAD+ synthetase belongs to the ...

    Nicotinamide adenine dinucleotide (NAD+) has a central role in life processes. The ubiquitous enzyme NAD+ synthetase catalyzes a key step in NAD+ biosynthesis, transforming deamido-NAD+ into NAD+ by a two-step reaction. NAD+ synthetase belongs to the amidotransferase family and has been recognized as a member of the family of N-type ATP pyrophosphatases. In order to investigate the mechanism of the reaction carried out by NAD+ synthetase we have determined a high-resolution three-dimensional structure of the Bacillus subtilis homodimeric NAD+ synthetase in complex with the trapped reaction intermediate NAD-adenylate.


    Related Citations: 
    • The Outb Gene of Bacillus Subtilis Codes for Nad Synthetase
      Nessi, C.,Albertini, A.M.,Speranza, M.L.,Galizzi, A.
      (1995) J.Biol.Chem. 270: 6181
    • 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

    Department of Pharmaceutical Science and Technology University of Torino, Italy. rizzi@ipvgen.unipv.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (NAD SYNTHETASE)
A, B
271Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: nadE (outB)
EC: 6.3.1.5
Find proteins for P08164 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P08164
Small Molecules
Ligands 5 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.480α = 90.00
b = 85.620β = 110.76
c = 60.120γ = 90.00
Software Package:
Software NamePurpose
CCP4model building
REFMACrefinement
CCP4phasing
MOSFLMdata reduction
ROTAVATAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description