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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.

April 2004 / First entry.

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

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

Sequences known to belong to this class detected by the profile: ALL Other sequence(s) detected in Swiss-Prot: NONE

• Domain architecture view of Swiss-Prot proteins matching PS50975 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50975 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50975 • Scan Swiss-Prot/TrEMBL entries against PS50975 • view ligand binding statistics

Matching PDB structures: 1A9X 1B6R 1B6S 1BNC ... [ALL]

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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