2Y5S

Crystal structure of Burkholderia cenocepacia dihydropteroate synthase complexed with 7,8-dihydropteroate.

• PDB DOI:  https://doi.org/10.2210/pdb2Y5S/pdb

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


• Deposited: 2011-01-17 Released: 2011-01-26 
• Deposition Author(s): Morgan, R.E., Batot, G.O., Dement, J.M., Rao, V.A., Eadsforth, T.C., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Crystal Structures of Burkholderia Cenocepacia Dihydropteroate Synthase in the Apo-Form and Complexed with the Product 7,8-Dihydropteroate.

Morgan, R.E., Batot, G.O., Dement, J.M., Rao, V.A., Eadsforth, T.C., Hunter, W.N.

(2011) BMC Struct Biol 11: 21

• PubMed: 21554707 
• DOI: https://doi.org/10.1186/1472-6807-11-21
• Primary Citation of Related Structures:  
  2Y5J, 2Y5S


• PubMed Abstract: 
  

The enzyme dihydropteroate synthase (DHPS) participates in the de novo synthesis of folate cofactors by catalyzing the formation of 7,8-dihydropteroate from condensation of p-aminobenzoic acid with 6-hydroxymethyl-7,8-dihydropteroate pyrophosphate. DHPS is absent from humans, who acquire folates from diet, and has been validated as an antimicrobial therapeutic target by chemical and genetic means. The bacterium Burkholderia cenocepacia is an opportunistic pathogen and an infective agent of cystic fibrosis patients. The organism is highly resistant to antibiotics and there is a recognized need for the identification of new drugs against Burkholderia and related Gram-negative pathogens. Our characterization of the DHPS active site and interactions with the enzyme product are designed to underpin early stage drug discovery.

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Organizational Affiliation: 

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 63.7 kDa 
• Atom Count: 4,665 
• Modelled Residue Count: 561 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROPTEROATE SYNTHASE	A, B	294	Burkholderia cenocepacia	Mutation(s): 0  EC: 2.5.1.15
UniProt
Find proteins for B4E5F5 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4E5F5  Go to UniProtKB:  B4E5F5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
78H	C [auth A], P [auth B]	7,8-DIHYDROPTEROATE C14 H14 N6 O3 WBFYVDCHGVNRBH-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.662	α = 90
b = 86.92	β = 90
c = 88.795	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Morgan, R.E., Batot, G.O., Dement, J.M., Rao, V.A., Eadsforth, T.C., Hunter, W.N.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references, Version format compliance