3TYU

Crystal Structure of Dihydropteroate synthetase with Product1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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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, 3TZF, 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, computational, and mutagenesis studies on the catalytic and resistance mechanisms of DHPS ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
7,8-dihydropteroate synthaseA, B280Yersinia pestisMutation(s): 0 
Gene Names: dhpS, folP, y0683, YPO3501, YP_0582, G4D65_15230, G4D67_06080, GD372_03005
EC: 2.5.1.15
UniProt
Find proteins for A0A2S9PLG4 (Yersinia pestis)
Explore A0A2S9PLG4 
Go to UniProtKB:  A0A2S9PLG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2S9PLG4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT1
Query on PT1
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		PTEROIC ACID
C14 H12 N6 O3
JOAQINSXLLMRCV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.75α = 90
b = 50.536β = 90.72
c = 74.495γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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