1EE1

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE ATP, TWO MOLECULES DEAMIDO-NAD+ AND ONE MG2+ ION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 806-812

  • Primary Citation of Related Structures:  1FYD, 1IFX, 1IH8

  • PubMed Abstract: 
  • The NH(3)-dependent NAD(+) synthetase (NADS) participates in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) by transforming nicotinic acid adenine dinucleotide (NaAD) to NAD(+). The structural behavior of the active site, including st ...

    The NH(3)-dependent NAD(+) synthetase (NADS) participates in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) by transforming nicotinic acid adenine dinucleotide (NaAD) to NAD(+). The structural behavior of the active site, including stabilization of flexible loops 82-87 and 204-225, has been studied by determination of the crystal structures of complexes of NADS with natural substrates and a substrate analog. Both loops are stabilized independently of NaAD and solely from the ATP-binding site. Analysis of the binding contacts suggests that the minor loop 82-87 is stabilized primarily by a hydrogen bond with the adenine base of ATP. Formation of a coordination complex with Mg(2+) in the ATP-binding site may contribute to the stabilization of the major loop 204-225. The major loop has a role in substrate recognition and stabilization, in addition to the protection of the reaction intermediate described previously. A second and novel Mg(2+) position has been observed closer to the NaAD-binding site in the structure crystallized at pH 7.5, where the enzyme is active. This could therefore be the catalytically active Mg(2+).


    Related Citations: 
    • Catalytic Cycle of NAD+ Synthetase Viewed by X-Ray Structures of Kinetic Intermediates
      Devedjiev, Y.,Singh, R.,Brouillette, C.,Muccio, D.,Brouillette, W.,DeLucas, L.,Jedzejas, M.
      (1998) AM.CRYST.ASSOC.,ABSTR.PAPERS (SUMMER MEETING) --: --
    • Asymmetric Complex of NAD+ Synthetase with Natural Substrates ATP Deamido-NAD+
      Devedjiev, Y.,Singh, R.,Brouillette, C.,Muccio, D.,Brouillette, W.,DeLucas, L.,Jedzejas, M.
      (1997) AM.CRYST.ASSOC.,ABSTR.PAPERS (SUMMER MEETING) --: --


    Organizational Affiliation

    Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
DND
Query on DND

Download SDF File 
Download CCD File 
A, B
NICOTINIC ACID ADENINE DINUCLEOTIDE
DEAMIDO-NAD+
C21 H27 N6 O15 P2
SENPVEZBRZQVST-HISDBWNOSA-O
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.980α = 90.00
b = 86.690β = 111.18
c = 60.480γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description