PROSITE documentation PDOC50975

ATP-grasp domain profile




Description

The ATP-grasp superfamily currently includes 17 groups of enzymes, catalyzing ATP-dependent ligation of a carboxylate containing molecule to an amino or thiol group-containing molecule [1]. They contribute predominantly to macromolecular synthesis. ATP-hydrolysis is used to activate a substrate. For example, DD-ligase transfers phosphate from ATP to D-alanine on the first step of catalysis. On the second step the resulting acylphosphate is attacked by a second D-alanine to produce a DD dipeptide following phosphate elimination [2].

The ATP-grasp domain contains three conserved motifs, corresponding to the phosphate binding loop and the Mg(2+) binding site [3]. The fold is characterized by two α-β subdomains that grasp the ATP molecule between them (see <PDB:1IOW>). Each subdomain provides a variable loop that forms a part of the active site, completed by region of other domains not conserved between the various ATP-grasp enzymes[4].

Proteins known to contain an ATP-grasp domain are listed below:

  • Biotin carboxylase (EC 6.3.4.14).
  • Carbamoyl-phosphate synthase (EC 6.3.5.5).
  • Cyanophycin synthetase (EC 6.-.-.-).
  • D-alanine--D-alanine ligase (EC 6.3.2.4).
  • Urea amidolyase (Urea carboxylase) (EC 6.3.4.6).
  • Glutathione synthetase (EC 6.3.2.3).
  • Lysine biosynthesis protein.
  • Methylcrotonyl-CoA carboxylase (EC 6.4.1.4).
  • MurC/ddl bifunctional enzyme (EC 6.3.2.8).
  • Propionyl-CoA carboxylase (EC 6.4.1.3).
  • Phosphoribosylamine--glycine ligase (EC 6.3.4.13).
  • Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21).
  • Pyruvate carboxylase 1 (EC 6.4.1.1).
  • CAD protein, includes carbamoyl-phosphate synthase activity.
  • Ribosomal protein S6 modification protein.
  • Succinyl-CoA synthetase (EC 6.2.1.5).
  • Vancomycin/teicoplanin resistance protein (EC 6.3.2.-).
  • 5-(carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18).
  • Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134).
  • Inositol-1,3,4-trisphosphate 5/6-kinase (EC 2.7.1.159).

The profile we developed covers the entire ATP-grasp domain.

Last update:

April 2004 / First entry.

Technical section

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

ATP_GRASP, PS50975; ATP-grasp fold profile  (MATRIX)


References

1AuthorsGalperin M.Y., Koonin E.V.
TitleA diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity.
SourceProtein Sci. 6:2639-2643(1997).
PubMed ID9416615

2AuthorsFan C., Moews P.C., Walsh C.T., Knox J.R.
TitleVancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution.
SourceScience 266:439-443(1994).
PubMed ID7939684

3AuthorsMurzin A.G.
TitleStructural classification of proteins: new superfamilies.
SourceCurr. Opin. Struct. Biol. 6:386-394(1996).
PubMed ID8804825

4AuthorsFan C., Moews P.C., Shi Y., Walsh C.T., Knox J.R.
TitleA common fold for peptide synthetases cleaving ATP to ADP: glutathione synthetase and D-alanine:d-alanine ligase of Escherichia coli.
SourceProc. Natl. Acad. Sci. U.S.A. 92:1172-1176(1995).
PubMed ID7862655



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