2G6W

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

• PDB DOI: https://doi.org/10.2210/pdb2G6W/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

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

• PubMed: 16557306 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 41.95 kDa 
• Atom Count: 3,142 
• Modelled Residue Count: 383 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-amino-7-oxononanoate synthase	A	384	Escherichia coli	Mutation(s): 0  EC: 2.3.1.47
UniProt
Find proteins for P12998 (Escherichia coli (strain K12)) Explore P12998  Go to UniProtKB:  P12998

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LLF	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 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.67	α = 90
b = 58.67	β = 90
c = 198.97	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  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
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary