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 
  • R-Value Observed: 0.179 

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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: https://doi.org/10.1039/b517922j
  • Primary Citation of Related Structures:  
    2G6W

  • 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 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
8-amino-7-oxononanoate synthase384Escherichia coliMutation(s): 0 
EC: 2.3.1.47
UniProt
Find proteins for P12998 (Escherichia coli (strain K12))
Explore P12998 
Go to UniProtKB:  P12998
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12998
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LLF
Query on LLF
Download Ideal Coordinates CCD File 
B [auth A](4-{(E)-[(2,2-DIFLUOROETHYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
C10 H13 F2 N2 O5 P
OXVHZSPVJUCFDH-QLKAYGNNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.67α = 90
b = 58.67β = 90
c = 198.97γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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