Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 61.20 kDa 
• Atom Count: 4502 
• Modelled Residue Count: 521 
• Deposited Residue Count: 549 
• Unique protein chains: 1

4BQH

Crystal structure of the uridine diphosphate N-acetylglucosamine pyrophosphorylase from Trypanosoma brucei in complex with inhibitor

• PDB DOI: 10.2210/pdb4BQH/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma brucei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-30 Released: 2013-07-17 
• Deposition Author(s): Fang, W., Raimi, O.G., vanAalten, D.M.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Literature

A Novel Allosteric Inhibitor of the Uridine Diphosphate N-Acetylglucosamine Pyrophosphorylase from Trypanosoma Brucei.

Urbaniak, M.D., Collie, I.T., Fang, W., Aristotelous, T., Eskilsson, S., Raimi, O.G., Harrison, J., Hopkins Navratolova, I., Frearson, J.A., Van Aalten, D.M.F., Ferguson, M.A.J.

(2013) ACS Chem Biol 8: 1981

• PubMed: 23834437 
• DOI: 10.1021/cb400411x
• Primary Citation of Related Structures:  
  4BQH


• PubMed Abstract: 
  

Uridine diphosphate N-acetylglucosamine pyrophosphorylase (UAP) catalyzes the final reaction in the biosynthesis of UDP-GlcNAc, an essential metabolite in many organisms including Trypanosoma brucei, the etiological agent of Human African Trypanosomiasis. High-throughput screening of recombinant T. brucei UAP identified a UTP-competitive inhibitor with selectivity over the human counterpart despite the high level of conservation of active site residues. Biophysical characterization of the UAP enzyme kinetics revealed that the human and trypanosome enzymes both display a strictly ordered bi-bi mechanism, but with the order of substrate binding reversed. Structural characterization of the T. brucei UAP-inhibitor complex revealed that the inhibitor binds at an allosteric site absent in the human homologue that prevents the conformational rearrangement required to bind UTP. The identification of a selective inhibitory allosteric binding site in the parasite enzyme has therapeutic potential.

---

Organizational Affiliation: 

Division of Biological Chemistry and Drug Discovery, ‡Division of Molecular Microbiology, and §MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee , Dundee DD1 5EH, U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE	A	549	Trypanosoma brucei	Mutation(s): 0  EC: 2.7.7.23
UniProt
Find proteins for Q386Q8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q386Q8  Go to UniProtKB:  Q386Q8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9VU	C [auth A]	(3S)-3-[2-(1,3-benzodioxol-5-yl)-2-oxidanylidene-ethyl]-4-bromanyl-5-methyl-3-oxidanyl-1H-indol-2-one C18 H14 Br N O5 SJXSNMXBXJIRLV-SFHVURJKSA-N
SO4	B [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
9VU	PDBBind:  4BQH	Kd: 2580 (nM) from 1 assay(s)
	Binding MOAD:  4BQH	Kd: 2580 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.93	α = 90
b = 103	β = 90
c = 187.14	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-30 
• Released Date: 2013-07-17 
Deposition Author(s): Fang, W., Raimi, O.G., vanAalten, D.M.F.

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references