1ECC

ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE COMPLEXED WITH MN-CPRPP AND 5-OXO-NORLEUCINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site.

Krahn, J.M.Kim, J.H.Burns, M.R.Parry, R.J.Zalkin, H.Smith, J.L.

(1997) Biochemistry 36: 11061-11068

  • DOI: https://doi.org/10.1021/bi9714114
  • Primary Citation of Related Structures:  
    1ECB, 1ECC

  • PubMed Abstract: 

    Activation of gluatmine phosphoribosylpyrophosphate (RPPP) amidotransferase (GPATase) by binding of a PRPP substrate analog results in the formation of a 20 A channel connecting the active site for glutamine hydrolysis in one domain with the PRPP site in a second domain. This solvent-inaccessible channel permits transfer of the NH3 intermediate between the two active sites. Tunneling of NH3 may be a common mechanism for glutamine amidotransferase-catalyzed nitrogen transfer and for coordination of catalysis at two distinct active sites in complex enzymes. The 2.4 A crystal structure of the active conformer of GPATase also provides the first description of an intact active site for the phosphoribosyltransferase (PRTase) family of nucleotide synthesis and salvage enzymes. Chemical assistance to catalysis is provided primarily by the substrate and secondarily by the enzyme in the proposed structure-based mechanism. Different catalytic and inhibitory modes of divalent cation binding to the PRTase active site are revealed in the active conformer of the enzyme and in a feedback-inhibited GMP complex.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
A, B
504Escherichia coliMutation(s): 0 
Gene Names: PURF
EC: 2.4.2.14
UniProt
Find proteins for P0AG16 (Escherichia coli (strain K12))
Explore P0AG16 
Go to UniProtKB:  P0AG16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG16
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCP
Query on PCP

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE
C6 H15 O13 P3
OICBXEWBKALHHB-MOJAZDJTSA-N
ONL
Query on ONL

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
5-OXO-L-NORLEUCINE
C6 H11 N O3
KSIJECNNZVKMJG-YFKPBYRVSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B],
I [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.2α = 90
b = 78.2β = 90
c = 308.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
HKLdata reduction
HKLdata scaling
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Other, Refinement description