PROSITE documentation PDOC50975ATP-grasp domain profile
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.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Galperin M.Y. Koonin E.V. |
| Title | A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. | |
| Source | Protein Sci. 6:2639-2643(1997). | |
| PubMed ID | 9416615 |
| 2 | Authors | Fan C. Moews P.C. Walsh C.T. Knox J.R. |
| Title | Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution. | |
| Source | Science 266:439-443(1994). | |
| PubMed ID | 7939684 |
| 3 | Authors | Murzin A.G. |
| Title | Structural classification of proteins: new superfamilies. | |
| Source | Curr. Opin. Struct. Biol. 6:386-394(1996). | |
| PubMed ID | 8804825 |
| 4 | Authors | Fan C. Moews P.C. Shi Y. Walsh C.T. Knox J.R. |
| Title | A common fold for peptide synthetases cleaving ATP to ADP: glutathione synthetase and D-alanine:d-alanine ligase of Escherichia coli. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 92:1172-1176(1995). | |
| PubMed ID | 7862655 |
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