3TYZ

Crystal Structure of the Yersinia pestis Dihydropteroate synthetase with substrate transition state complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 

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:  

  • 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 pestisMutation(s): 0 
Gene Names: dhpS
EC: 2.5.1.15
Find proteins for Q7CKJ1 (Yersinia pestis)
Go to UniProtKB:  Q7CKJ1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAB
Query on PAB

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Download CCD File 
A, B
4-AMINOBENZOIC ACID
C7 H7 N O2
ALYNCZNDIQEVRV-UHFFFAOYSA-N
 Ligand Interaction
POP
Query on POP

Download SDF File 
Download CCD File 
A, B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
XHP
Query on XHP

Download SDF File 
Download CCD File 
A, B
2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one
C7 H7 N5 O
CHIXTMVYEYYHIG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.179α = 90.00
b = 50.522β = 90.75
c = 74.668γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DENZOdata reduction
MAR345dtbdata collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-09-26 
  • Released Date: 2012-03-14 
  • Deposition Author(s): Wu, Y.

Revision History 

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