PROSITE documentation PDOC00665Glycine radical domain signature and profile
Protein radicals are components of several biologically important reactions. Glycyl radical enzymes are involved in a great variety of functions, for example, nucleotide, pyruvate and toluene metabolism [1]. These enzymes are posttranslationally interconverted, under anaerobic conditions, from an inactive to an active form that carries a stable radical localized to a specific glycine at the C-terminal region of the polypeptidic chain. Extreme sensitivity towards destruction by oxygen, leading to polypeptide cleavage between the N-Cα bond of the Gly residue, is a conspicuous property of all protein-based glycyl radicals, thus confining their existence to strictly anaerobic conditions.
Some proteins known to contain a glycyl radical are listed below:
- Escherichia coli pyruvate formate-lyase (EC 2.3.1.54) (genes pflB, pflD and pflF), a key enzyme of anaerobic glucose metabolism, it converts pyruvate and CoA into acetyl-CoA and pyruvate [2].
- Escherichia coli (gene nrdD) and bacteriophage T4 (gene nrdD or sunY) anaerobic ribonucleoside-triphosphate reductase (EC 1.17.4.2) [3,4].
- Escherichia coli and bacteriophage T4 autonomous glycyl radical cofactor (gene grcA) [5].
These proteins share a conserved region centered around the glycine which, in pfl, is known to bear the free radical. We use this region has a signature pattern. We also developed a profile which covers the entire glycine radical domain.
Last update:April 2006 / Pattern revised.
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PROSITE methods (with tools and information) covered by this documentation:
| 1 | Authors | Eklund H. Fontecave M. |
| Title | Glycyl radical enzymes: a conservative structural basis for radicals. | |
| Source | Structure 7:R257-R262(1999). | |
| PubMed ID | 10574800 |
| 2 | Authors | Wagner A.F.V. Frey M. Neugebauer F.A. Schaefer W. Knappe J. |
| Title | The free radical in pyruvate formate-lyase is located on glycine-734. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 89:996-1000(1992). | |
| PubMed ID | 1310545 |
| 3 | Authors | Sun X. Harder J. Krook M. Joernvall H. Sjoeberg B.-M. Reichard P. |
| Title | A possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 90:577-581(1993). | |
| PubMed ID | 8421692 |
| 4 | Authors | Young P. Oehman M. Xu M.Q. Shub D.A. Sjoeberg B.-M. |
| Title | Intron-containing T4 bacteriophage gene sunY encodes an anaerobic ribonucleotide reductase. | |
| Source | J. Biol. Chem. 269:20229-20232(1994). | |
| PubMed ID | 8051113 |
| 5 | Authors | Wagner A.F.V. Schultz S. Bomke J. Pils T. Lehmann W.D. Knappe J. |
| Title | YfiD of Escherichia coli and Y06I of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase. | |
| Source | Biochem. Biophys. Res. Commun. 285:456-462(2001). | |
| PubMed ID | 11444864 | |
| DOI | 10.1006/bbrc.2001.5186 |
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