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 
  • R-Value Observed: 0.154 

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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 D Biol Crystallogr 57: 806-812

  • DOI: 10.1107/s0907444901003523
  • Primary Citation of Related Structures:  
    1EE1, 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 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 ...

    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: 
    • 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) --: --
    • 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) --: --

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NH(3)-DEPENDENT NAD(+) SYNTHETASEA, B271Bacillus subtilisMutation(s): 0 
Gene Names: nadE
EC: 6.3.5.1 (PDB Primary Data), 6.3.1.5 (UniProt)
UniProt
Find proteins for P08164 (Bacillus subtilis (strain 168))
Explore P08164 
Go to UniProtKB:  P08164
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DND (Subject of Investigation/LOI)
Query on DND

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]NICOTINIC ACID ADENINE DINUCLEOTIDE
C21 H27 N6 O15 P2
SENPVEZBRZQVST-HISDBWNOSA-O
 Ligand Interaction
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth 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 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.98α = 90
b = 86.69β = 111.18
c = 60.48γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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