3PFL

CRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE ANALOGUE OXAMATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase.

Becker, A.Fritz-Wolf, K.Kabsch, W.Knappe, J.Schultz, S.Volker Wagner, A.F.

(1999) Nat.Struct.Mol.Biol. 6: 969-975

  • DOI: 10.1038/13341
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyruvate formate-lyase (PFL) from Escherichia coli uses a radical mechanism to reversibly cleave the C1-C2 bond of pyruvate using the Gly 734 radical and two cysteine residues (Cys 418, Cys 419). We have determined by X-ray crystallography the struct ...

    Pyruvate formate-lyase (PFL) from Escherichia coli uses a radical mechanism to reversibly cleave the C1-C2 bond of pyruvate using the Gly 734 radical and two cysteine residues (Cys 418, Cys 419). We have determined by X-ray crystallography the structures of PFL (non-radical form), its complex with the substrate analog oxamate, and the C418A,C419A double mutant. The atomic model (a dimer of 759-residue monomers) comprises a 10-stranded beta/alpha barrel assembled in an antiparallel manner from two parallel five-stranded beta-sheets; this architecture resembles that of ribonucleotide reductases. Gly 734 and Cys 419, positioned at the tips of opposing hairpin loops, meet in the apolar barrel center (Calpha-Sgamma = 3.7 A). Oxamate fits into a compact pocket where C2 is juxtaposed with Cys 418Sgamma (3.3 A), which in turn is close to Cys 419Sgamma (3.7 A). Our model of the active site is suggestive of a snapshot of the catalytic cycle, when the pyruvate-carbonyl awaits attack by the Cys 418 thiyl radical. We propose a homolytic radical mechanism for PFL that involves Cys 418 and Cys 419 both as thiyl radicals, with distinct chemical functions.


    Organizational Affiliation

    Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Jahnstrabe 29, 69120 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (FORMATE ACETYLTRANSFERASE 1)
A, B
759Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pflB (pfl)
EC: 2.3.1.54
Find proteins for P09373 (Escherichia coli (strain K12))
Go to UniProtKB:  P09373
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXM
Query on OXM

Download SDF File 
Download CCD File 
A, B
OXAMIC ACID
C2 H3 N O3
SOWBFZRMHSNYGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 159.210α = 90.00
b = 159.210β = 90.00
c = 160.270γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-31
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance