Putative AMP-binding domain signature

It has been shown [1,2,3,4,5] that a number of prokaryotic and eukaryotic enzymes which all probably act via an ATP-dependent covalent binding of AMP to their substrate, share a region of sequence similarity. These enzymes are:

• Insects luciferase (luciferin 4-monooxygenase) (EC 1.13.12.7). Luciferase produces light by catalyzing the oxidation of luciferin in presence of ATP and molecular oxygen.
• α-aminoadipate reductase (EC 1.2.1.31) from yeast (gene LYS2). This enzyme catalyzes the activation of α-aminoadipate by ATP-dependent adenylation and the reduction of activated α-aminoadipate by NADPH.
• Acetate--CoA ligase (EC 6.2.1.1) (acetyl-CoA synthetase), an enzyme that catalyzes the formation of acetyl-CoA from acetate and CoA.
• Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3), an enzyme that activates long-chain fatty acids for both the synthesis of cellular lipids and their degradation via β-oxidation.
• 4-coumarate--CoA ligase (EC 6.2.1.12) (4CL), a plant enzyme that catalyzes the formation of 4-coumarate-CoA from 4-coumarate and coenzyme A; the branchpoint reactions between general phenylpropanoid metabolism and pathways leading to various specific end products.
• O-succinylbenzoic acid--CoA ligase (EC 6.2.1.26) (OSB-CoA synthetase) (gene menE) [6], a bacterial enzyme involved in the biosynthesis of menaquinone (vitamin K2).
• 4-Chlorobenzoate--CoA ligase (EC 6.2.1.-) (4-CBA--CoA ligase) [7], a Pseudomonas enzyme involved in the degradation of 4-CBA.
• Indoleacetate--lysine ligase (EC 6.3.2.20) (IAA-lysine synthetase) [8], an enzyme from Pseudomonas syringae that converts indoleacetate to IAA-lysine.
• Bile acid-CoA ligase (gene baiB) from Eubacterium strain VPI 12708 [4]. This enzyme catalyzes the ATP-dependent formation of a variety of C-24 bile acid-CoA.
• Crotonoβine/carnitine-CoA ligase (EC 6.3.2.-) from Escherichia coli (gene caiC).
• L-(α-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACV synthetase) from various fungi (gene acvA or pcbAB). This enzyme catalyzes the first step in the biosynthesis of penicillin and cephalosporin, the formation of ACV from the constituent amino acids. The amino acids seem to be activated by adenylation. It is a protein of around 3700 amino acids that contains three related domains of about 1000 amino acids.
• Gramicidin S synthetase I (gene grsA) from Bacillus brevis. This enzyme catalyzes the first step in the biosynthesis of the cyclic antibiotic gramicidin S, the ATP-dependent racemization of phenylalanine (EC 5.1.1.11)
• Tyrocidine synthetase I (gene tycA) from Bacillus brevis. The reaction carried out by tycA is identical to that catalyzed by grsA
• Gramicidin S synthetase II (gene grsB) from Bacillus brevis. This enzyme is a multifunctional protein that activates and polymerizes proline, valine, ornithine and leucine. GrsB consists of four related domains.
• Enterobactin synthetase components E (gene entE) and F (gene entF) from Escherichia coli. These two enzymes are involved in the ATP-dependent activation of respectively 2,3-dihydroxybenzoate and serine during enterobactin (enterochelin) biosynthesis.
• Cyclic peptide antibiotic surfactin synthase subunits 1, 2 and 3 from Bacillus subtilis. Subunits 1 and 2 contains three related domains while subunit 3 only contains a single domain.
• HC-toxin synthetase (gene HTS1) from Cochliobolus carbonum. This enzyme activates the four amino acids (Pro, L-Ala, D-Ala and 2-amino-9,10-epoxi-8- oxodecanoic acid) that make up HC-toxin, a cyclic tetrapeptide. HTS1 consists of four related domains.

There are also some proteins, whose exact function is not yet known, but which are, very probably, also AMP-binding enzymes. These proteins are:

• ORA (octapeptide-repeat antigen), a Plasmodium falciparum protein whose function is not known but which shows a high degree of similarity with the above proteins.
• AngR, a Vibrio anguillarum protein. AngR is thought to be a transcriptional activator which modulates the anguibactin (an iron-binding siderophore) biosynthesis gene cluster operon. But we believe [9], that angR is not a DNA-binding protein, but rather an enzyme involved in the biosynthesis of anguibactin. This conclusion is based on three facts: the presence of the AMP-binding domain; the size of angR (1048 residues), which is far bigger than any bacterial transcriptional protein; and the presence of a probable S-acyl thioesterase immediately downstream of angR.
• A hypothetical protein in mmsB 3'region in Pseudomonas aeruginosa.
• Escherichia coli hypothetical protein ydiD.
• Yeast hypothetical protein YBR041w.
• Yeast hypothetical protein YBR222c.
• Yeast hypothetical protein YER147c.

All these proteins contains a highly conserved region very rich in glycine, serine, and threonine which is followed by a conserved lysine. A parallel can be drawn [9] between this type of domain and the G-x(4)-G-K-[ST] ATP-/ GTP-binding 'P-loop' domain or the protein kinases G-x-G-x(2)-[SG]-x(10,20)-K ATP-binding domains (see <PDOC00017> and <PDOC00100>).