Biological Assembly 1  

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

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 204.18 kDa 
• Atom Count: 14152 
• Modelled Residue Count: 1820 
• Deposited Residue Count: 1836 
• Unique protein chains: 1

1AO0

GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE FROM B. SUBTILIS COMPLEXED WITH ADP AND GMP

• PDB DOI: 10.2210/pdb1AO0/pdb

• Classification: GLUTAMINE AMIDOTRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-07-15 Released: 1997-11-12 
• Deposition Author(s): Tomchick, D.R., Smith, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Literature

Mechanism of the synergistic end-product regulation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase by nucleotides.

Chen, S., Tomchick, D.R., Wolle, D., Hu, P., Smith, J.L., Switzer, R.L., Zalkin, H.

(1997) Biochemistry 36: 10718-10726

• PubMed: 9271502 
• DOI: 10.1021/bi9711893
• Primary Citation of Related Structures:  
  1AO0


• PubMed Abstract: 
  

De novo purine nucleotide synthesis is regulated, at least in part, by end-product inhibition of glutamine PRPP amidotransferase. An important feature of this inhibition is the fact that certain synergistic nucleotide pairs give more than additive inhibition. The physiological importance of synergism is in amplifying regulation by the adenine and guanine nucleotide end products of de novo synthesis. Using a new method to quantitate synergism, ADP plus GMP were confirmed [Meyer, E., and Switzer, R. L. (1978) J. Biol. Chem. 254, 5397-5402] to give strong synergistic inhibition of Bacillus subtilis glutamine PRPP amidotransferase. An X-ray structure of the ternary enzyme.ADP.GMP complex established that ADP binds to the allosteric A site and GMP to the catalytic C site. GMP increased the binding affinity of ADP for the A site by approximately 20-fold. Synergism results from a specific nucleotide-nucleotide interaction that is dependent upon a nucleoside diphosphate in the A site and a nucleoside monophosphate in the C site. Furthermore, synergism is enhanced by the competition between nucleotide inhibitor and PRPP substrate for the C site. Purine base specificity results from a backbone carbonyl interaction of Lys305' with the 6-NH2 group of adenine in the A site and a Ser347 Ogamma interaction with the 2-NH2 group of guanine in the C site. Steric considerations favor binding of the nucleoside diphosphate to the A site. Site-directed replacements of key residues increased the nucleotide concentrations needed for 50% inhibition and in some cases perturbed synergism. Mutations in either of the nucleotide sites perturbed function at both sites, supporting the important role of synergism.

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Organizational Affiliation: 

Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE	A, B, C, D	459	Bacillus subtilis	Mutation(s): 0  Gene Names: purF EC: 2.4.2.14
UniProt
Find proteins for P00497 (Bacillus subtilis (strain 168)) Explore P00497  Go to UniProtKB:  P00497

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	H [auth A], L [auth B], P [auth C], T [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
5GP	G [auth A], K [auth B], O [auth C], S [auth D]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
SF4	F [auth A], J [auth B], N [auth C], R [auth D]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
MG	E [auth A], I [auth B], M [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ADP	PDBBind:  1AO0	Kd: 1.10e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.3	α = 90
b = 70.4	β = 90
c = 182.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
HKL	data reduction
HKL	data scaling
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-07-15 
• Released Date: 1997-11-12 
Deposition Author(s): Tomchick, D.R., Smith, J.L.

Revision History  

• Version 1.0: 1997-11-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance