Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 61260.02 
• Atom Count: 3826 
• Residue Count: 560 
• Unique protein chains: 1

3TYU

Crystal Structure of Dihydropteroate synthetase with Product1

• DOI: 10.2210/pdb3TYU/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2011-09-26 Released: 2012-03-14 
• Deposition Author(s): Yun, M.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.264 
• R-Value Work: 0.210 

Literature

Catalysis and sulfa drug resistance in dihydropteroate synthase.

Yun, M.K., Wu, Y., Li, Z., Zhao, Y., Waddell, M.B., Ferreira, A.M., Lee, R.E., Bashford, D., White, S.W.

(2012) Science 335: 1110-1114

• PubMed: 22383850 
• DOI: 10.1126/science.1214641
• Primary Citation of Related Structures:  
  3V5O, 3TZN, 3TZF, 3TYZ, 3TYE, 3TYD, 3TYC, 3TYB, 3TYA


• PubMed Abstract: 
  

The sulfonamide antibiotics inhibit dihydropteroate synthase (DHPS), a key enzyme in the folate pathway of bacteria and primitive eukaryotes. However, resistance mutations have severely compromised the usefulness of these drugs. We report structural, computational, and mutagenesis studies on the catalytic and resistance mechanisms of DHPS. By performing the enzyme-catalyzed reaction in crystalline DHPS, we have structurally characterized key intermediates along the reaction pathway. Results support an S(N)1 reaction mechanism via formation of a novel cationic pterin intermediate. We also show that two conserved loops generate a substructure during catalysis that creates a specific binding pocket for p-aminobenzoic acid, one of the two DHPS substrates. This substructure, together with the pterin-binding pocket, explains the roles of the conserved active-site residues and reveals how sulfonamide resistance arises.

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Organizational Affiliation: 

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
7,8-dihydropteroate synthase	A, B	280	Yersinia pestis	Mutation(s): 0  Gene Names: dhpS EC: 2.5.1.15
Find proteins for Q7CKJ1 (Yersinia pestis) Go to UniProtKB:  Q7CKJ1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PT1	A, B	PTEROIC ACID C14 H12 N6 O3 JOAQINSXLLMRCV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.264 
• R-Value Work: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 70.750	α = 90.00
b = 50.536	β = 90.72
c = 74.495	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
MAR345dtb	data collection
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-26 
• Released Date: 2012-03-14 
• Deposition Author(s): Yun, M.K.

Revision History 

• Version 1.0: 2012-03-14
  Type: Initial release
• Version 1.1: 2017-11-08
  Type: Refinement description