The domain within your query sequence starts at position 372 and ends at position 398; the E-value for the PLDc domain shown below is 6.11e0.
WARNING! Some of the required catalytic sites were not detected in this domain. It is probably inactive! Check the literature (PubMed 10074947 ) for details.
Catalytic residues
Position
Amino acid
Present?
Domain
Protein
6
377
H
No
13
384
D
Yes
FPKLNRNKYMVTDGAAYIGNFDWVGND
PLDc
Phospholipase D. Active site motifs.
SMART accession number:
SM00155
Description:
Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.
Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site aspartic acid. An Escherichia coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs [ (PUBMED:8732763) (PUBMED:8755242) (PUBMED:8051126) (PUBMED:9242915) ].
Crystal structure of a phospholipase D family member.
Nat Struct Biol. 1999; 6: 278-84
Display abstract
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.
Phospholipase D: enzymology, mechanisms of regulation, and function.
Physiol Rev. 1997; 77: 303-20
Display abstract
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.
Annu Rev Biochem. 1997; 66: 475-509
Display abstract
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 novel family of phospholipase D homologues that includes phospholipid synthases and putative endonucleases: identification of duplicated repeats and potential active site residues.
Protein Sci. 1996; 5: 914-22
Display abstract
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.
J Biol Chem. 1994; 269: 20312-7
Display abstract
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.
Metabolism (metabolic pathways involving proteins which contain this domain)
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This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with PLDc domain which could be assigned to a KEGG orthologous group, and not all proteins containing PLDc domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.
