Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 64.40 kDa 
• Atom Count: 4651 
• Modelled Residue Count: 558 
• Deposited Residue Count: 568 
• Unique protein chains: 1

2PZA

NAD+ Synthetase from Bacillus anthracis with AMP + PPi and Mg2+

• PDB DOI: 10.2210/pdb2PZA/pdb

• Classification: LIGASE
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-17 Released: 2007-07-31 
• Deposition Author(s): McDonald, H.M., Pruett, P.S., Deivanayagam, C., Protasevich, I.I., Carson, W.M., DeLucas, L.J., Brouillette, W.J., Brouillette, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Literature

Structural adaptation of an interacting non-native C-terminal helical extension revealed in the crystal structure of NAD(+) synthetase from Bacillus anthracis.

McDonald, H.M., Pruett, P.S., Deivanayagam, C., Protasevich, I.I., Carson, W.M., DeLucas, L.J., Brouillette, W.J., Brouillette, C.G.

(2007) Acta Crystallogr D Biol Crystallogr 63: 891-905

• PubMed: 17642516 
• DOI: 10.1107/S0907444907029769
• Primary Citation of Related Structures:  
  2PZ8, 2PZA, 2PZB


• PubMed Abstract: 
  

The crystal structures of NH(3)-dependent NAD+ synthetase from Bacillus anthracis as the apoenzyme (1.9 A), in complex with the natural catalytic products AMP and pyrophosphate (2.4 A) and in complex with the substrate analog adenosine 5'-(alpha,beta-methylene)triphosphate (2.0 A) have been determined. NAD+ synthetase catalyzes the last step in the biosynthesis of the vitally important cofactor NAD+. In comparison to other NAD+ synthetase crystal structures, the C-terminal His-tagged end of the apoenzyme adopts a novel helical conformation, causing significant compensatory changes in the region. The structural accommodations observed in B. anthracis NAD+ synthetase are remarkable in the absence of adverse affects on enzyme activity. They also illustrate a rare example of the influence of a non-native C-terminal His-tag extension on the structure of a native protein. In contrast to the apoenzyme, when AMP and pyrophosphate or adenosine 5'-(alpha,beta-methylene)triphosphate are bound, the C-terminus adopts a conformation that allows ATP binding and overall the structure then resembles other NAD+ synthetase structures. The structures of NAD+ synthetase complexes from B. anthracis are compared with published X-ray crystal structures of the enzyme from B. subtilis, Escherichia coli and Helicobacter pylori. These comparisons support the novel observation that P1 and P2 loop ordering is not a consequence of crystal contacts but rather a consequence of intrinsic intramolecular interactions within the ordered subunit.

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Organizational Affiliation: 

Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294-4440, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A, B	284	Bacillus anthracis	Mutation(s): 0  Gene Names: nadE, BA_1998, GBAA_1998, BAS1855 EC: 6.3.1.5
UniProt
Find proteins for Q81RP3 (Bacillus anthracis) Explore Q81RP3  Go to UniProtKB:  Q81RP3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	E [auth A], J [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
POP	F [auth A], K [auth B]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
GOL	G [auth A], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], D [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.046	α = 90
b = 96.375	β = 90
c = 68.612	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
StructureStudio	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-17 
• Released Date: 2007-07-31 
Deposition Author(s): McDonald, H.M., Pruett, P.S., Deivanayagam, C., Protasevich, I.I., Carson, W.M., DeLucas, L.J., Brouillette, W.J., Brouillette, C.G.

Revision History  

• Version 1.0: 2007-07-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance