1ECG

DON INACTIVATED ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and function of the glutamine phosphoribosylpyrophosphate amidotransferase glutamine site and communication with the phosphoribosylpyrophosphate site.

Kim, J.H.Krahn, J.M.Tomchick, D.R.Smith, J.L.Zalkin, H.

(1996) J.Biol.Chem. 271: 15549-15557


  • PubMed Abstract: 
  • Glutamine phosphoribosylpyrophosphate (PRPP) amidotransferase from Escherichia coli exhibits a basal PRPP-independent glutaminase activity having a kcat/Km that is 0.3% of fully active enzyme. Binding of PRPP activates the enzyme by a structural chan ...

    Glutamine phosphoribosylpyrophosphate (PRPP) amidotransferase from Escherichia coli exhibits a basal PRPP-independent glutaminase activity having a kcat/Km that is 0.3% of fully active enzyme. Binding of PRPP activates the enzyme by a structural change that lowers the Km for glutamine 100-fold and couples glutamine hydrolysis to synthesis of 5-phosphoribosylamine. By analysis of the x-ray structure of the glutamine site containing bound 6-diazo-5-oxonorleucine, a glutamine affinity analog, and by site-directed mutagenesis we have identified residues important for glutamine binding, catalysis, and coupling with PRPP. Tyr74 is a key residue in the coupling between the sites for glutamine in the NH2-terminal domain and PRPP in the COOH-terminal domain. Arg73 and Asp127 have roles in glutamine binding. The x-ray structure indicates that there are no amino acid side chains sufficiently close to Cys1 to participate as a proton acceptor in formation of the thiolate needed for nucleophilic attack on the carboxamide of glutamine, nor as a general acid for amide nitrogen transfer. Based on the x-ray model of the glutamine site and analysis of a mutant enzyme we propose that the free NH2 terminus of Cys1 functions as the proton acceptor and donor. The results indicate that the side chain of Asn101 and the backbone nitrogen of Gly102 function to stabilize a tetrahedral oxyanion resulting from attack of Cys1 on the glutamine carboxamide. Cys1, Arg73, Asn101, Gly102, and Asp127 are conserved in the NH2-terminal domain of a subfamily of amidotransferases that includes asparagine synthetase, glucosamine 6-phosphate synthase, and glutamate synthase, implying a common function in the four enzymes. Tyr74, on the other hand, is conserved only in glutamine PRPP amidotransferase sequences consistent with a specific role in interdomain coupling. The catalytic framework of key glutamine site residues supports the assignment of glutamine PRPP amidotransferase to a recently described Ntn (NH2-terminal nucleophile) hydrolase family of enzymes.


    Organizational Affiliation

    Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-1153, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
A, B
504Escherichia coli (strain K12)Gene Names: purF
EC: 2.4.2.14
Find proteins for P0AG16 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG16
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PIN
Query on PIN

Download SDF File 
Download CCD File 
A, B
PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
PIPES; 1,4-PIPERAZINEDIETHANESULFONIC ACID
C8 H18 N2 O6 S2
IHPYMWDTONKSCO-UHFFFAOYSA-N
 Ligand Interaction
ONL
Query on ONL

Download SDF File 
Download CCD File 
A, B
5-OXO-L-NORLEUCINE
C6 H11 N O3
KSIJECNNZVKMJG-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.147 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 116.900α = 90.00
b = 157.500β = 90.00
c = 106.300γ = 90.00
Software Package:
Software NamePurpose
HKLdata reduction
HKLdata scaling
X-PLORphasing
X-PLORrefinement
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1996-04-23 
  • Released Date: 1996-11-08 
  • Deposition Author(s): Krahn, J.M.

Revision History 

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model