Biological Assembly 1  

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

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 34.06 kDa 
• Atom Count: 2230 
• Modelled Residue Count: 288 
• Deposited Residue Count: 299 
• Unique protein chains: 1

1H3D

STRUCTURE OF THE E.COLI ATP-PHOSPHORIBOSYLTRANSFERASE

• PDB DOI: 10.2210/pdb1H3D/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-08-27 Released: 2003-10-03 
• Deposition Author(s): Lohkamp, B., McDermott, G., Coggins, J.R., Lapthorn, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.277 
• R-Value Work: 0.222 
• R-Value Observed: 0.226 

Literature

The Structure of Escherichia Coli ATP-Phosphoribosyltransferase: Identification of Substrate Binding Sites and Mode of AMP Inhibition

Lohkamp, B., Mcdermott, G., Campbell, S., Coggins, J.R., Lapthorn, A.J.

(2004) J Mol Biol 336: 131

• PubMed: 14741209 
• DOI: 10.1016/j.jmb.2003.12.020
• Primary Citation of Related Structures:  
  1H3D, 1Q1K


• PubMed Abstract: 
  

ATP-phosphoribosyltransferase (ATP-PRT), the first enzyme of the histidine pathway, is a complex allosterically regulated enzyme, which controls the flow of intermediates through this biosynthetic pathway. The crystal structures of Escherichia coli ATP-PRT have been solved in complex with the inhibitor AMP at 2.7A and with product PR-ATP at 2.9A (the ribosyl-triphosphate could not be resolved). On the basis of binding of AMP and PR-ATP and comparison with type I PRTs, the PRPP and parts of the ATP-binding site are identified. These structures clearly identify the AMP as binding in the 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP)-binding site, with the adenosine ring occupying the ATP-binding site. Comparison with the recently solved Mycobacterium tuberculosis ATP-PRT structures indicates that histidine is solely responsible for the large conformational changes observed between the hexameric forms of the enzyme. The role of oligomerisation in inhibition and the structural basis for the synergistic inhibition by histidine and AMP are discussed.

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Organizational Affiliation: 

Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-PHOSPHORIBOSYLTRANSFERASE	A	299	Escherichia coli K-12	Mutation(s): 0  Gene Names: hisG, b2019, JW2001 EC: 2.4.2.17
UniProt
Find proteins for P60757 (Escherichia coli (strain K12)) Explore P60757  Go to UniProtKB:  P60757

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
TLA	C [auth A], D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.277 
• R-Value Work: 0.222 
• R-Value Observed: 0.226 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.645	α = 90
b = 133.645	β = 90
c = 114.118	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-08-27 
• Released Date: 2003-10-03 
Deposition Author(s): Lohkamp, B., McDermott, G., Coggins, J.R., Lapthorn, A.J.

Revision History  

• Version 1.0: 2003-10-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance