1C9D

CRYSTAL STRUCTURE OF THE COMPLEX OF BACTERIAL TRYPTOPHAN SYNTHASE WITH THE TRANSITION STATE ANALOGUE INHIBITOR 4-(2-HYDROXY-4-FLUOROPHENYLTHIO)-BUTYLPHOSPHONIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic studies of phosphonate-based alpha-reaction transition-state analogues complexed to tryptophan synthase.

Sachpatzidis, A.Dealwis, C.Lubetsky, J.B.Liang, P.H.Anderson, K.S.Lolis, E.

(1999) Biochemistry 38: 12665-12674

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In an effort to use a structure-based approach for the design of new herbicides, the crystal structures of complexes of tryptophan synthase with a series of phosphonate enzyme inhibitors were determined at 2.3 A or higher resolution. These inhibitors ...

    In an effort to use a structure-based approach for the design of new herbicides, the crystal structures of complexes of tryptophan synthase with a series of phosphonate enzyme inhibitors were determined at 2.3 A or higher resolution. These inhibitors were designed to mimic the transition state formed during the alpha-reaction of the enzyme and, as expected, have affinities much greater than that of the natural substrate indole-3-glycerol phosphate or its nonhydrolyzable analogue indole propanol phosphate (IPP). These inhibitors are ortho-substituted arylthioalkylphosphonate derivatives that have an sp(3)-hybridized sulfur atom, designed to mimic the putative tetrahedral transition state at the C3 atom of the indole, and lack the C2 atom to allow for higher conformational flexibility. Overall, the inhibitors bind in a fashion similar to that of IPP. Glu-49 and Phe-212 are the two active site residues whose conformation changes upon inhibitor binding. A very short hydrogen bond between a phosphonate oxygen and the Ser-235 hydroxyl oxygen may be responsible for stabilization of the enzyme-inhibitor complexes. Implications for the mechanism of catalysis as well as directions for more potent inhibitors are discussed.


    Related Citations: 
    • Three-Dimensional Structure of the Tryptophan Synthase Alpha 2 Beta 2 Multienzyme Complex from Salmonella typhimurium
      Hyde, C.C.,Ahmed, S.A.,Padlan, E.A.,Miles, E.W.,Davies, D.R.
      (1988) J.Biol.Chem. 263: 17857
    • Loop Closure and Intersubunit Communication in Tryptophan Synthase
      Schneider, T.R.,Gerhardt, E.,Lee, M.,Liang, P.H.,Anderson, K.S.,Schlichting, I.
      (1998) Biochemistry 37: 5394


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPTOPHAN SYNTHASE (ALPHA CHAIN)
A
268Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: trpA
EC: 4.2.1.20
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P00929
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRYPTOPHAN SYNTHASE (BETA CHAIN)
B
397Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: trpB
EC: 4.2.1.20
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P0A2K1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HF1
Query on HF1

Download SDF File 
Download CCD File 
A
4-(2-HYDROXY-4-FLUOROPHENYLTHIO)-BUTYLPHOSPHONIC ACID
C10 H12 F O4 P S
UXOYJQMPYTYCMG-ORCRQEGFSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HF1IC50: 499 nM BINDINGMOAD
HF1IC50: 499 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.220α = 90.00
b = 60.520β = 94.43
c = 67.790γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
CCP4data scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance