2F3O

Crystal Structure of a glycyl radical enzyme from Archaeoglobus fulgidus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a glycyl radical enzyme from Archaeoglobus fulgidus

Lehtio, L.Grossmann, J.G.Kokona, B.Fairman, R.Goldman, A.

(2006) J Mol Biol 357: 221-235

  • DOI: 10.1016/j.jmb.2005.12.049
  • Primary Citation of Related Structures:  
    2F3O

  • PubMed Abstract: 
  • We have solved the crystal structure of a PFL2 from Archaeglobus fulgidus at 2.9 A resolution. Of the three previously solved enzyme structures of glycyl radical enzymes, pyruvate formate lyase (PFL), anaerobic ribonucleotide reductase and glycerol dehydratase (GD), the last one is clearly most similar to PFL2 ...

    We have solved the crystal structure of a PFL2 from Archaeglobus fulgidus at 2.9 A resolution. Of the three previously solved enzyme structures of glycyl radical enzymes, pyruvate formate lyase (PFL), anaerobic ribonucleotide reductase and glycerol dehydratase (GD), the last one is clearly most similar to PFL2. We observed electron density in the active site of PFL2, which we modelled as glycerol. The orientation of the glycerol is different from that in GD, and changes in the active site indicate that the actual substrate of PFL2 is bigger than a glycerol molecule, but sequence and structural homology suggest that PFL2 may be a dehydratase. Crystal packing, solution X-ray scattering and ultracentrifugation experiments show that PFL2 is tetrameric, unlike other glycyl radical enzymes. A.fulgidus is a hyperthermophile and PFL2 appears to be stabilized by several factors including an increased number of ion pairs, differences in buried charges, a truncated N terminus, anchoring of loops and N terminus via salt-bridges, changes in the oligomeric interface and perhaps also the higher oligomerization state of the protein.


    Organizational Affiliation

    Institute of Biotechnology, University of Helsinki, PO Box 65, FIN-00014, Helsinki, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
pyruvate formate-lyase 2A, B776Archaeoglobus fulgidusMutation(s): 0 
Gene Names: AF1449PFLD
UniProt
Find proteins for O28823 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28823 
Go to UniProtKB:  O28823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28823
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.03α = 90
b = 174.17β = 90
c = 162.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description