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,PQS (software)

Macromolecule Content

• Total Structure Weight: 41.88 kDa 
• Atom Count: 2800 
• Modelled Residue Count: 338 
• Deposited Residue Count: 364 
• Unique protein chains: 1

1G9S

CRYSTAL STRUCTURE OF A COMPLEX BETWEEN E.COLI HPRT AND IMP

• PDB DOI: 10.2210/pdb1G9S/pdb

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


• Deposited: 2000-11-27 Released: 2002-08-28 
• Deposition Author(s): Guddat, L.W., Vos, S., Martin, J.L., Keough, D.T., de Jersey, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.243 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 

Literature

Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase.

Guddat, L.W., Vos, S., Martin, J.L., Keough, D.T., de Jersey, J.

(2002) Protein Sci 11: 1626-1638

• PubMed: 12070315 
• DOI: 10.1110/ps.0201002
• Primary Citation of Related Structures:  
  1G9S, 1G9T, 1GRV


• PubMed Abstract: 
  

Crystal structures have been determined for free Escherichia coli hypoxanthine phosphoribosyltransferase (HPRT) (2.9 A resolution) and for the enzyme in complex with the reaction products, inosine 5'-monophosphate (IMP) and guanosine 5'-monophosphate (GMP) (2.8 A resolution). Of the known 6-oxopurine phosphoribosyltransferase (PRTase) structures, E. coli HPRT is most similar in structure to that of Tritrichomonas foetus HGXPRT, with a rmsd for 150 Calpha atoms of 1.0 A. Comparison of the free and product bound structures shows that the side chain of Phe156 and the polypeptide backbone in this vicinity move to bind IMP or GMP. A nonproline cis peptide bond, also found in some other 6-oxopurine PRTases, is observed between Leu46 and Arg47 in both the free and complexed structures. For catalysis to occur, the 6-oxopurine PRTases have a requirement for divalent metal ion, usually Mg(2+) in vivo. In the free structure, a Mg(2+) is coordinated to the side chains of Glu103 and Asp104. This interaction may be important for stabilization of the enzyme before catalysis. E. coli HPRT is unique among the known 6-oxopurine PRTases in that it exhibits a marked preference for hypoxanthine as substrate over both xanthine and guanine. The structures suggest that its substrate specificity is due to the modes of binding of the bases. In E. coli HPRT, the carbonyl oxygen of Asp163 would likely form a hydrogen bond with the 2-exocyclic nitrogen of guanine (in the HPRT-guanine-PRib-PP-Mg(2+) complex). However, hypoxanthine does not have a 2-exocyclic atom and the HPRT-IMP structure suggests that hypoxanthine is likely to occupy a different position in the purine-binding pocket.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, School of Molecular and Microbial Science, The University of Queensland, St. Lucia, Qld. 4072, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE	A, B	182	Escherichia coli	Mutation(s): 0  Gene Names: hpt EC: 2.4.2.8
UniProt
Find proteins for P0A9M2 (Escherichia coli (strain K12)) Explore P0A9M2  Go to UniProtKB:  P0A9M2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMP	C [auth A]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
N	D [auth B]	ANY 5'-MONOPHOSPHATE NUCLEOTIDE C5 H11 O7 P CYZZKTRFOOKUMT-LMVFSUKVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IMP	PDBBind:  1G9S	Ki: 2.47e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.243 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.14	α = 90
b = 84.14	β = 90
c = 167.27	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-11-27 
• Released Date: 2002-08-28 
Deposition Author(s): Guddat, L.W., Vos, S., Martin, J.L., Keough, D.T., de Jersey, J.

Revision History  

• Version 1.0: 2002-08-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance