3CB8

4Fe-4S-Pyruvate formate-lyase activating enzyme in complex with AdoMet and a peptide substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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)Mutation(s): 0 
Gene Names: pflA (act)
EC: 1.97.1.4
Find proteins for P0A9N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9N4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide substrate VSGYAV
B
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

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Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 74.494α = 90.00
b = 74.494β = 90.00
c = 187.737γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
HKL-2000data reduction
CNSrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
SCALEITdata scaling

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