2F3O

Crystal Structure of a glycyl radical enzyme from Archaeoglobus fulgidus

Summary for 2F3O

• Entry DOI: 10.2210/pdb2f3o/pdb
• Descriptor: pyruvate formate-lyase 2, TRIETHYLENE GLYCOL, GLYCEROL, ... (4 entities in total)
• Functional Keywords: pyruvate formate lyase, glycerol dehydratase, pfl2, glycyl radical, hyperthermophilic, unknown function
• Biological source: Archaeoglobus fulgidus
• Total number of polymer chains: 2
• Total formula weight: 175013.49

Authors

Lehtio, L.,Goldman, A. (deposition date: 2005-11-22, release date: 2006-03-07, Last modification date: 2023-08-23)

Primary citation

Lehtio, L.,Grossmann, J.G.,Kokona, B.,Fairman, R.,Goldman, A.
Crystal structure of a glycyl radical enzyme from Archaeoglobus fulgidus
J.Mol.Biol., 357:221-235, 2006

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 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.

PubMed: 16414072
DOI: 10.1016/j.jmb.2005.12.049

Experimental method

X-RAY DIFFRACTION (2.9 Å)