3C8F

4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.

Vey, J.L.Yang, J.Li, M.Broderick, W.E.Broderick, J.B.Drennan, C.L.

(2008) Proc.Natl.Acad.Sci.Usa 105: 16137-16141

  • DOI: 10.1073/pnas.0806640105
  • Primary Citation of Related Structures:  3CB8

  • PubMed Abstract: 
  • Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase perform ...

    Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.


    Organizational Affiliation

    Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate formate-lyase 1-activating enzyme
A
245Escherichia coli (strain K12)Gene Names: pflA (act)
EC: 1.97.1.4
Find proteins for P0A9N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9N4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MT2
Query on MT2

Download SDF File 
Download CCD File 
A
[(3S)-3-amino-3-carboxypropyl](ethyl)methylsulfonium
S-ethyl-L-Methionine
C7 H16 N O2 S
CHUUUZMZGJUUGS-UPONEAKYSA-O
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.224 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 58.051α = 90.00
b = 58.051β = 90.00
c = 117.466γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
DENZOdata reduction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SOLVEphasing
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-05-14
    Type: Atomic model
  • Version 1.3: 2017-10-25
    Type: Refinement description