Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 26.29 kDa 
• Atom Count: 2064 
• Modelled Residue Count: 236 
• Deposited Residue Count: 236 
• Unique protein chains: 1

1QCC

CRYSTAL STRUCTURES OF ADENINE PHOSPHORIBOSYLTRANSFERASE FROM LEISHMANIA DONOVANI

• PDB DOI: 10.2210/pdb1QCC/pdb

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


• Deposited: 1999-05-01 Released: 1999-07-21 
• Deposition Author(s): Phillips, C.L., Ullman, B., Brennan, R.G., Hill, C.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.241 
• R-Value Work: 0.187 

Literature

Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani.

Phillips, C.L., Ullman, B., Brennan, R.G., Hill, C.P.

(1999) EMBO J 18: 3533-3545

• PubMed: 10393170 
• DOI: 10.1093/emboj/18.13.3533
• Primary Citation of Related Structures:  
  1QB7, 1QB8, 1QCC, 1QCD


• PubMed Abstract: 
  

The enzyme adenine phosphoribosyltransferase (APRT) functions to salvage adenine by converting it to adenosine-5-monophosphate (AMP). APRT deficiency in humans is a well characterized inborn error of metabolism, and APRT may contribute to the indispensable nutritional role of purine salvage in protozoan parasites, all of which lack de novo purine biosynthesis. We determined crystal structures for APRT from Leishmania donovani in complex with the substrate adenine, the product AMP, and sulfate and citrate ions that appear to mimic the binding of phosphate moieties. Overall, these structures are very similar to each other, although the adenine and AMP complexes show different patterns of hydrogen-bonding to the base, and the active site pocket opens slightly to accommodate the larger AMP ligand. Whereas AMP adopts a single conformation, adenine binds in two mutually exclusive orientations: one orientation providing adenine-specific hydrogen bonds and the other apparently positioning adenine for the enzymatic reaction. The core of APRT is similar to that of other phosphoribosyltransferases, although the adenine-binding domain is quite different. A C-terminal extension, unique to Leishmania APRTs, extends an extensive dimer interface by wrapping around the partner molecule. The active site involves residues from both subunits of the dimer, indicating that dimerization is essential for catalysis.

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Organizational Affiliation: 

Biochemistry Department, University of Utah, Salt Lake City, UT 84132, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENINE PHOSPHORIBOSYLTRANSFERASE	A	236	Leishmania donovani	Mutation(s): 0  Gene Names: LDHU3_26.0190 EC: 2.4.2.7
UniProt
Find proteins for Q27679 (Leishmania donovani) Explore Q27679  Go to UniProtKB:  Q27679

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.241 
• R-Value Work: 0.187 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.757	α = 90
b = 63.757	β = 90
c = 236.617	γ = 120

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-01 
• Released Date: 1999-07-21 
Deposition Author(s): Phillips, C.L., Ullman, B., Brennan, R.G., Hill, C.P.

Revision History  

• Version 1.0: 1999-07-21
  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