3TYE

Dihydropteroate Synthase in complex with DHP-STZ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydropteroate synthase
A, B
297Bacillus anthracis str. A2012Mutation(s): 0 
Gene Names: folPBAS0071BA_0071GBAA_0071
EC: 2.5.1.15
UniProt
Find proteins for Q81VW8 (Bacillus anthracis)
Explore Q81VW8 
Go to UniProtKB:  Q81VW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81VW8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XTZ
Query on XTZ

Download Ideal Coordinates CCD File 
C [auth A]4-{[(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)methyl]amino}-N-(1,3-thiazol-2-yl)benzenesulfonamide
C16 H16 N8 O3 S2
XKJZNFKQXDBJHJ-UHFFFAOYSA-N
YTZ
Query on YTZ

Download Ideal Coordinates CCD File 
I [auth B]4-amino-N-(1,3-thiazol-2-yl)benzenesulfonamide
C9 H9 N3 O2 S2
JNMRHUJNCSQMMB-UHFFFAOYSA-N
XHP
Query on XHP

Download Ideal Coordinates CCD File 
H [auth B]2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one
C7 H7 N5 O
CHIXTMVYEYYHIG-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.329α = 90
b = 97.329β = 90
c = 263.829γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Non-polymer description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description