Taxonomic distribution of proteins containing PLDc domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing PLDc domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Crystal structure of a phospholipase D family member.

Stuckey JA, Dixon JE
Nat Struct Biol. 1999; 6: 278-84

The first crystal structure of a phospholipase D (PLD) family member has been determined at 2.0 A resolution. The PLD superfamily is defined by a common sequence motif, HxK(x)4D(x)6GSxN, and includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. The crystal structure suggests that residues from two sequence motifs form a single active site. A histidine residue from one motif acts as a nucleophile in the catalytic mechanism, forming a phosphoenzyme intermediate, whereas a histidine residue from the other motif appears to function as a general acid in the cleavage of the phosphodiester bond. The structure suggests that the conserved lysine residues are involved in phosphate binding. Large-scale genomic sequencing revealed that there are many PLD family members. Our results suggest that all of these proteins may possess a common structure and catalytic mechanism.

New developments in phospholipase D.

Exton JH
J Biol Chem. 1997; 272: 15579-82

Phospholipase D: enzymology, mechanisms of regulation, and function.

Exton JH
Physiol Rev. 1997; 77: 303-20

Phospholipase D exists in various forms that differ in their regulation but predominantly hydrolyze phosphatidylcholine. The Ca(2+)-dependent isozymes of protein kinase C regulate phospholipase D in vitro and play a major role in its control by growth factors and G protein-linked agonists in vivo. Recent studies have demonstrated that small G proteins of the ADP-ribosylation factor (ARF) and Rho families activate the enzyme in vitro, and evidence is accumulating that they also are involved in its control in vivo. Both types of G protein play important roles in cellular function, and the possible mechanisms by which they are activated by agonists are discussed. There is also emerging evidence of the control of phospholipase D and Rho proteins by soluble tyrosine kinases and novel serine/threonine kinases. The possible role of these kinases in agonist regulation of phospholipase D is discussed. The function of phospholipase D in cells is still poorly defined. Postulated roles of phosphatidic acid produced by phospholipase D action include the activation of Ca(2+)-independent isoforms of protein kinase C, the regulation of growth and the cytoskeleton in fibroblasts, and control of the respiratory burst in neutrophils. Another important function of phosphatidic acid is to act as a substrate for a specific phospholipase A2 to generate lysophosphatidic acid, which is becoming increasingly recognized as a major intercellular messenger. Finally, it is possible that the phospholipid changes induced in various cellular membranes by phospholipase D may per se play an important role in vesicle trafficking and other membrane-associated events.

Regulation of eukaryotic phosphatidylinositol-specific phospholipase C and phospholipase D.

Singer WD, Brown HA, Sternweis PC
Annu Rev Biochem. 1997; 66: 475-509

This review focuses on two phospholipase activities involved in eukaryotic signal transduction. The action of the phosphatidylinositol-specific phospholipase C enzymes produces two well-characterized second messengers, inositol 1,4,5-trisphosphate and diacylglycerol. This discussion emphasizes recent advances in elucidation of the mechanisms of regulation and catalysis of the various isoforms of these enzymes. These are especially related to structural information now available for a phospholipase C delta isozyme. Phospholipase D hydrolyzes phospholipids to produce phosphatidic acid and the respective head group. A perspective of selected past studies is related to emerging molecular characterization of purified and cloned phospholipases D. Evidence for various stimulatory agents (two small G protein families, protein kinase C, and phosphoinositides) suggests complex regulatory mechanisms, and some studies suggest a role for this enzyme activity in intracellular membrane traffic.

A duplicated catalytic motif in a new superfamily of phosphohydrolases and phospholipid synthases that includes poxvirus envelope proteins.

Koonin EV
Trends Biochem Sci. 1996; 21: 242-3

A novel family of phospholipase D homologues that includes phospholipid synthases and putative endonucleases: identification of duplicated repeats and potential active site residues.

Ponting CP, Kerr ID
Protein Sci. 1996; 5: 914-22

Phosphatidylcholine-specific phospholipase D (PLD) enzymes catalyze hydrolysis of phospholipid phosphodiester bonds, and also transphosphatidylation of phospholipids to acceptor alcohols. Bacterial and plant PLD enzymes have not been shown previously to be homologues or to be homologous to any other protein. Here we show, using sequence analysis methods, that bacterial and plant PLDs show significant sequence similarities both to each other, and to two other classes of phospholipid-specific enzymes, bacterial cardiolipin synthases, and eukaryotic and bacterial phosphatidylserine synthases, indicating that these enzymes form an homologous family. This family is suggested also to include two Poxviridae proteins of unknown function (p37K and protein K4), a bacterial endonuclease (nuc), an Escherichia coli putative protein (o338) containing an N-terminal domain showing similarities with helicase motifs V and VI, and a Synechocystis sp. putative protein with a C-terminal domain likely to possess a DNA-binding function. Surprisingly, four regions of sequence similarity that occur once in nuc and o338, appear twice in all other homologues, indicating that the latter molecules are bi-lobed, having evolved from an ancestor or ancestors that underwent a gene duplication and fusion event. It is suggested that, for each of these enzymes, conserved histidine, lysine, aspartic acid, and/or asparagine residues may be involved in a two-step ping pong mechanism involving an enzyme-substrate intermediate.

Cloning and expression of phosphatidylcholine-hydrolyzing phospholipase D from Ricinus communis L.

Wang X, Xu L, Zheng L
J Biol Chem. 1994; 269: 20312-7

Phosphatidylcholine-hydrolyzing phospholipase D (PLD; EC 3.1.4.4) has been proposed to play an important role in the signal transduction pathways in animals and in various cellular processes in plants. To unravel the structure of PLD and further the investigation of its modes of regulation and cellular function, we have isolated a PLD cDNA from castor bean (Ricinus communis L. var. Hale) by using oligonucleotide probes based on the N-terminal amino acid sequence of purified PLD protein. The nucleotide sequence of the castor bean PLD cDNA clone contains an open reading frame of 2424 bases encoding an 808-amino acid protein of 92,400 daltons. Expression of this PLD cDNA clone in Escherichia coli resulted in the accumulation of a functional PLD able to catalyze hydrolysis and transphosphatidylation reactions, demonstrating that the introduction of this single gene product was sufficient to confer PLD activity and that both the hydrolysis and transphosphatidylation reactions are catalyzed the single PLD protein. Comparison of the deduced protein sequence of the clone to the N-terminal amino acid sequence of purified PLD revealed that the mature PLD protein is preceded by a 30-amino acid leader peptide. Removal of this leader peptide resulted in accumulation of non-functional PLD and also increased PLD degradation in E. coli, suggesting that this leader peptide may be involved in proper folding of PLD. The primary structure of the castor bean PLD exhibits no significant similarities with sequences of other cloned lipolytic enzymes.