This domain is found in a variety of bacterial extracellular proteins. Although initially described as having a divergent Ig fold this domain has a novel topology that is like a mirror image of the beta grasp fold. Hence the name of Mirror Beta Grasp (MBG) domain [].
Glutathionylspermidine (GSP) synthetases of Trypanosomatidae and Escherichia coli couple hydrolysis of ATP (to ADP and Pi) with formation of an amide bond between spermidine and the glycine carboxylate of glutathione (gamma-Glu-Cys-Gly). In the pathogenic trypanosomatids, this reaction is the penultimate step in the biosynthesis of the antioxidant metabolite, trypanothione (N1,N8-bis-(glutathionyl)spermidine), and is a target for drug design []. This domain, which is structurally related to the pre-ATP grasp domain, probably carries the substrate-binding site [].
Members of this family are ATP-grasp family enzymes related to a number of characterised glutamate ligases, including the ribosomal protein S6 modification enzyme RimK. This group belongs to a conserved gene neighbourhood that also features an HPr kinase-related protein. We assign this system the initial designation GAK, for Grasp (this ATP-grasp family enzyme), Amphipathic (for the member of the domain entry , designated Amphi-Trp), and Kinase, for the HPr-kinase homologue .
The Golgi apparatus is a highly dynamic organelle responsible for sorting out proteins and other biomolecules to the cell surface and to the extracellular milieu. The Golgi apparatus is comprised of flattened membrane-bound compartments called cisternae, which are apposed to one another to form a Golgi stack. The structural organization of the cisternae into stacks and their lateral connection, building the Golgi ribbon, requires a family of proteins called Golgi ReAssembly and Stacking Proteins (GRASP). Two homologues (GRASP55 and GRASP65) have been described in vertebrates and their functions have been associated to Golgi phosphorylation-regulated assembly/disassembly, protein secretion , Golgi remodeling in migrating cells, among others. There is only one gene for GRASP in lower eukaryotes. Essentially all GRASPs containa conserved N-terminal GRASP region, which comprises two tandem PDZ domains (PDZ1 and PDZ2), a classical protein-peptide interaction domain, and is responsible for GRASP homo-oligomerization and for the attachment to the Golgi membrane. The C-terminal half which is not conserved between species but is rich in proline and serines residues, as well as glutamine and asparagine residues [, , , ]. The GRASP-type PDZ domains adopt a canonical PDZ fold with a β-sandwich of five β-strands and two α-helices. The PDZ1 and PDZ2 domains are nearly superimposable. The peptide-binding pockets of both PDZ domains are formed by alpha2 and beta5. A typical ligand peptide is predicted to form antiparallel β-strand interactions with beta5 and insert hydrophobic side chains between alpha2 and beta5. The two PDZ domains cooperate to achieve dimerization and oligomerization. In the dimers the PDZ2 domains interact in a way that positions the peptide-binding pockets facing each other. In addition, the dimers are linked through interactions between the two C-terminal tails (CTs) of one dimer and two peptide-binding pockets of the PDZ1 domains in the next dimer [, ]. This entry represents the GRASP-type PDZ domain.
T6SS bacteria employ toxic effectors to inhibit rival cells and concurrently use effector cognate immunity proteins to protect their sibling cells. The effector and immunity pairs (E-I pairs) endow the bacteria with a great advantage in niche competition. This is the C-terminal domain of Tli4. The Tle cognate immunity proteins (Tlis) can directly disable the transported Tle protein and thereby mediate the self-protection process. The Tle-Tli effector-immunity (E-I) pairs confer substantial advantage to the donor cell during interbacterial competition. Tli4 displays a two-domain structure, in which a large lobe and a small lobe form a crab claw-like conformation. Tli4 uses this crab claw to grasp the cap domain of Tle4, especially the lid2 region, which prevents the interfacial activation of Tle4 and thus causes enzymatic dysfunction of Tle4. Structural comparison indicates similarity between this C-terminal domain of Tli4 and Tsi3, which is the cognate immunity protein of the effector protein Tse3 in P. aeruginosa PDB:4n7s [].
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 []. 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 [].The ATP-grasp domain contains three conserved motifs, corresponding to the phosphate binding loop and the Mg(2+) binding site []. The fold is characterised by two α-β subdomains that grasp the ATP molecule between them. Each subdomain provides a variable loop that formspart of the active site, with regions from other domains also contributing to the active site, even though these other domains are not conserved between the various ATP-grasp enzymes [].
The ATP-grasp superfamily currently includes 17 groups of enzymes, catalysing ATP-dependent ligation of a carboxylate containing molecule to an amino or thiol group-containing molecule []. 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 [].The ATP-grasp domain contains three conserved motifs, corresponding to the phosphate binding loop and the Mg(2+) binding site []. The fold is characterised by two α-β subdomains that grasp the ATP molecule between them. 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 [].The ATP-grasp domain represented by this entry is found primarily in succinyl-CoA synthetases ().
Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This family represents PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, which catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. PurK belongs to the ATP grasp superfamily of C-N ligase enzymes. Each subunit of PurK is composed of three domains (A, B, and C). The B domain contains a flexible, glycine-rich loop (B loop, T123-G130) that is disordered in the sulphate-PurK structure and becomes ordered in the MgADP-PurK structure. MgADP is wedged between the B and C domains, as with all members of the ATP grasp superfamily. Other enzymes in this superfamily contain a conserved Omega loop proposed to interact with the B loop, define the specificity of their nonnucleotide substrate, and protect the acyl phosphate intermediate formed from this substrate. PurK contains a minimal Omega loopwithout conserved residues. In the reaction catalyzed by PurK, carboxyphosphate is the putative acyl phosphate intermediate. The sulphate of the sulphate ion-liganded PurK interacts electrostatically with Arg 242 and the backbone amide group of Asn 245, components of the J loop of the C domain. This sulphate may reveal the location of the carboxyphosphate binding site. Conserved residues within the C terminus of the C domain define a pocket that is proposed to bind AIR in collaboration with an N-terminal strand loop helix motif in the A domain (P loop, G8-L1). The P loop is proposed to bind the phosphate of AIR on the basis of similar binding sites observed in PurN and PurE and proposed in PurD and PurT, four other enzymes in the purine pathway [].
The ATP-grasp fold is one of several distinct ATP-binding folds, and is found in enzymes that catalyze the formation of amide bonds, catalyzing the ATP-dependent ligation of a carboxylate-containing molecule to an amino or thiol group-containing molecule []. This fold is found in many differentenzyme families, including various peptide synthetases, biotin carboxylase, synapsin, succinyl-CoA synthetase, pyruvate phosphate dikinase, and glutathione synthetase, amongst others []. These enzymes contribute predominantly to macromolecular synthesis, using ATP-hydrolysis to activate their substrates. The ATP-grasp fold shares functional and structural similarities with the PIPK (phosphatidylinositol phosphate kinase) and protein kinase superfamilies. The ATP-grasp domain consists of two subdomains with different alpha+beta folds, which grasp the ATP molecule between them. Each subdomain provides a variable loop that forms part of the active site, with regions from other domains also contributing to the active site, even though these other domains are not conserved between the various ATP-grasp enzymes [].This entry describes a type of ATP-grasp fold such as that found in pyrrolysine biosynthesis protein PylC [].
The ATP-grasp fold is one of several distinct ATP-binding folds, and is found in enzymes that catalyse the formation of amide bonds, catalysing the ATP-dependent ligation of a carboxylate-containing molecule to an amino or thiol group-containing molecule []. This fold is found in many different enzyme families, including various peptide synthetases, biotin carboxylase, synapsin, succinyl-CoA synthetase, pyruvate phosphate dikinase, and glutathione synthetase, amongst others []. These enzymes contribute predominantly to macromolecular synthesis, using ATP-hydrolysis to activate their substrates. The ATP-grasp fold shares functional and structural similarities with the PIPK (phosphatidylinositol phosphate kinase) and protein kinase superfamilies. The ATP-grasp domain consists of two subdomains with different alpha+beta folds, which grasp the ATP molecule between them. Each subdomain provides a variable loop that forms part of the active site, with regions from other domains also contributing to the active site, even though these other domains are not conserved between the various ATP-grasp enzymes [].This entry represents subdomain 1 found at the N-terminal end of the ATP-grasp domain.
