2G6W

Suicide inhibition of a-Oxamine Synthase: Structures of the Covalent Adducts of 8-Amino-7-oxonanoate Synthase with trifluoroalanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Suicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine.

Alexeev, D.Baxter, R.L.Campopiano, D.J.Kerbarh, O.Sawyer, L.Tomczyk, N.Watt, R.Webster, S.P.

(2006) Org.Biomol.Chem. 4: 1209-1212

  • DOI: 10.1039/b517922j

  • PubMed Abstract: 
  • The irreversible inhibition of 8-amino-7-oxononanoate synthase by trifluoroalanine involves decarboxylative defluorination of the inhibitor-PLP aldimine followed by attack of the conjugated imine by the amino group of the active site lysine to afford ...

    The irreversible inhibition of 8-amino-7-oxononanoate synthase by trifluoroalanine involves decarboxylative defluorination of the inhibitor-PLP aldimine followed by attack of the conjugated imine by the amino group of the active site lysine to afford a covalently bound difluorinated intermediate which can subsequently undergo further HF losses and hydrolysis to afford a 2-(pyridoximine phosphate) acetoyl protein adduct.


    Organizational Affiliation

    School of Biology, Swann Building, University of Edinburgh, Mayfield Road, Edinburgh, UKEH9 3JR.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
8-amino-7-oxononanoate synthase
A
384Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: bioF
EC: 2.3.1.47
Find proteins for P12998 (Escherichia coli (strain K12))
Go to UniProtKB:  P12998
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LLF
Query on LLF

Download SDF File 
Download CCD File 
A
(4-{(E)-[(2,2-DIFLUOROETHYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
(E)-N-(2,2-DIFLUOROETHYL)PYRIDOXIMINE-5'-PHOSPHATE
C10 H13 F2 N2 O5 P
OXVHZSPVJUCFDH-QLKAYGNNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.176 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 58.670α = 90.00
b = 58.670β = 90.00
c = 198.970γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-02-26 
  • Released Date: 2006-04-25 
  • Deposition Author(s): Alexeev, D.

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description