PROSITE documentation PDOC00665

Glycine radical domain signature and profile




Description

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.

Technical section

PROSITE methods (with tools and information) covered by this documentation:

GLY_RADICAL_2, PS51149; Glycine radical domain profile  (MATRIX)

GLY_RADICAL_1, PS00850; Glycine radical domain signature  (PATTERN)


References

1AuthorsEklund H., Fontecave M.
TitleGlycyl radical enzymes: a conservative structural basis for radicals.
SourceStructure 7:R257-R262(1999).
PubMed ID10574800

2AuthorsWagner A.F.V., Frey M., Neugebauer F.A., Schaefer W., Knappe J.
TitleThe free radical in pyruvate formate-lyase is located on glycine-734.
SourceProc. Natl. Acad. Sci. U.S.A. 89:996-1000(1992).
PubMed ID1310545

3AuthorsSun X., Harder J., Krook M., Joernvall H., Sjoeberg B.-M., Reichard P.
TitleA possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene.
SourceProc. Natl. Acad. Sci. U.S.A. 90:577-581(1993).
PubMed ID8421692

4AuthorsYoung P., Oehman M., Xu M.Q., Shub D.A., Sjoeberg B.-M.
TitleIntron-containing T4 bacteriophage gene sunY encodes an anaerobic ribonucleotide reductase.
SourceJ. Biol. Chem. 269:20229-20232(1994).
PubMed ID8051113

5AuthorsWagner A.F.V., Schultz S., Bomke J., Pils T., Lehmann W.D., Knappe J.
TitleYfiD of Escherichia coli and Y06I of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase.
SourceBiochem. Biophys. Res. Commun. 285:456-462(2001).
PubMed ID11444864
DOI10.1006/bbrc.2001.5186



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