3TZF

Crystal Structure of the Yersinia pestis Dihydropteroate Synthase with Sulfonamide Drug Complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

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

  • 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, ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
7,8-dihydropteroate synthase
A, B
280Yersinia pestisGene Names: folP (dhpS)
EC: 2.5.1.15
Find proteins for Q7CKJ1 (Yersinia pestis)
Go to UniProtKB:  Q7CKJ1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HH2
Query on HH2

Download SDF File 
Download CCD File 
A, B
6-HYDROXYMETHYLPTERIN-DIPHOSPHATE
[PTERIN-6-YL METHANYL]-PHOSPHONOPHOSPHATE
C7 H9 N5 O8 P2
AMDUVUKDRBIVAH-UHFFFAOYSA-N
 Ligand Interaction
08D
Query on 08D

Download SDF File 
Download CCD File 
B
Sulfamethoxazole
4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide, SMX, SMZ
C10 H11 N3 O3 S
JLKIGFTWXXRPMT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.245α = 90.00
b = 50.582β = 90.80
c = 74.988γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-09-27 
  • Released Date: 2012-03-14 
  • Deposition Author(s): Wu, Y.

Revision History 

  • Version 1.0: 2012-03-14
    Type: Initial release