1GPH | pdb_00001gph

STRUCTURE OF THE ALLOSTERIC REGULATORY ENZYME OF PURINE BIOSYNTHESIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 
    0.182 (Depositor) 
  • R-Value Observed: 
    0.182 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1GPH

This is version 1.5 of the entry. See complete history

Literature

Structure of the allosteric regulatory enzyme of purine biosynthesis.

Smith, J.L.Zaluzec, E.J.Wery, J.P.Niu, L.Switzer, R.L.Zalkin, H.Satow, Y.

(1994) Science 264: 1427-1433

  • DOI: https://doi.org/10.1126/science.8197456
  • Primary Citation Related Structures: 
    1GPH

  • PubMed Abstract: 

    Multi-wavelength anomalous diffraction (MAD) has been used to determine the structure of the regulatory enzyme of de novo synthesis of purine nucleotides, glutamine 5-phosphoribosyl-1-pyrophosphate (PRPP) amidotransferase, from Bacillus subtilis. This allosteric enzyme, a 200-kilodalton tetramer, is subject to end product regulation by purine nucleotides. The metalloenzyme from B. subtilis is a paradigm for the higher eukaryotic enzymes, which have been refractory to isolation in stable form. The two folding domains of the polypeptide are correlated with functional domains for glutamine binding and for transfer of ammonia to the substrate PRPP. Eight molecules of the feedback inhibitor adenosine monophosphate (AMP) are bound to the tetrameric enzyme in two types of binding sites: the PRPP catalytic site of each subunit and an unusual regulatory site that is immediately adjacent to each active site but is between subunits. An oxygen-sensitive [4Fe-4S] cluster in each subunit is proposed to regulate protein turnover in vivo and is distant from the catalytic site. Oxygen sensitivity of the cluster is diminished by AMP, which blocks a channel through the protein to the cluster. The structure is representative of both glutamine amidotransferases and phosphoribosyltransferases.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.

Macromolecule Content 

  • Total Structure Weight: 206.21 kDa 
  • Atom Count: 14,372 
  • Modeled Residue Count: 1,860 
  • Deposited Residue Count: 1,860 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASEA [auth 1],
B [auth 2],
C [auth 3],
D [auth 4]
465Bacillus subtilisMutation(s): 0 
EC: 2.4.2.14
UniProt
Find proteins for P00497 (Bacillus subtilis (strain 168))
Explore P00497 
Go to UniProtKB:  P00497
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00497
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4

Query on SF4



Download:Ideal Coordinates CCD File
E [auth 1],
H [auth 2],
K [auth 3],
N [auth 4]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
AMP

Query on AMP



Download:Ideal Coordinates CCD File
F [auth 1]
G [auth 1]
I [auth 2]
J [auth 2]
L [auth 3]
F [auth 1],
G [auth 1],
I [auth 2],
J [auth 2],
L [auth 3],
M [auth 3],
O [auth 4],
P [auth 4]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work:  0.182 (Depositor) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.8α = 90
b = 75.7β = 91.4
c = 94.1γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 1994-07-31 
  • Deposition Author(s): Smith, J.L.

Revision History  (Full details and data files)

  • Version 1.0: 1994-07-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2014-05-21
    Changes: Structure summary
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.5: 2024-02-07
    Changes: Data collection, Database references, Derived calculations