phospholipase D-like domain-containing protein may hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group, and may also catalyze the transphosphatidylation of phospholipids to acceptor alcohols
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ...
66-335
1.86e-166
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.
The actual alignment was detected with superfamily member cd09183:
Pssm-ID: 472788 Cd Length: 274 Bit Score: 481.27 E-value: 1.86e-166
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence ...
66-335
1.86e-166
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83C; N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83C (FAM83C). Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. The N-terminus of FAM83C shows high homology to other FAM83 family members, indicating that FAM83C might have arisen early in vertebrate evolution by duplication of a gene in the FAM83 family.
Pssm-ID: 197280 Cd Length: 274 Bit Score: 481.27 E-value: 1.86e-166
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence ...
66-335
1.86e-166
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83C; N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83C (FAM83C). Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. The N-terminus of FAM83C shows high homology to other FAM83 family members, indicating that FAM83C might have arisen early in vertebrate evolution by duplication of a gene in the FAM83 family.
Pssm-ID: 197280 Cd Length: 274 Bit Score: 481.27 E-value: 1.86e-166
N-terminal phospholipase D-like domain of proteins from the Family with sequence similarity 83; ...
66-335
6.56e-134
N-terminal phospholipase D-like domain of proteins from the Family with sequence similarity 83; N-terminal phospholipase D (PLD)-like domain of vetebrate proteins from the Family with sequence similarity 83 (FAM83), which is comprised of 8 members, designated FAM83A through FAM83H. Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, the FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are unlikely to carry PLD activity. Members of the FAM83 are mostly uncharacterized proteins. FAM83A, also known as tumor antigen BJ-TSA-9, is a novel tumor-specific gene highly expressed in human lung adenocarcinoma. FAM83D, also known as spindle protein CHICA, is a cell-cycle-regulated spindle component which localizes to the mitotic spindle and is both upregulated and phosphorylated during mitosis. The gene encoding protein FAM83H is the first gene involved in the etiology of amelogenesis imperfecta (AI), that encodes a non-secreted protein due to the absence of a signal peptide. Defects in gene FAM83H cause autosomal dominant hypocalcified amelogenesis imperfecta (ADHCAI). FAM83B, FAM83C, FAM83F, and FAM83G are uncharacterized proteins present across vertebrates while FAM83E is an uncharacterized protein found only in mammals.
Pssm-ID: 197218 Cd Length: 269 Bit Score: 397.52 E-value: 6.56e-134
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence ...
71-340
4.41e-87
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83A; N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83A (FAM83A), also known as tumor antigen BJ-TSA-9. FAM83A or BJ-TSA-9 is a novel tumor-specific gene highly expressed in human lung adenocarcinoma. Due to this specific expression pattern, it may serve as a biomarker for lung cancer, especially in the early detection of micrometastasis for lung adenocarcinoma patients. Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity.
Pssm-ID: 197278 Cd Length: 276 Bit Score: 276.31 E-value: 4.41e-87
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence ...
86-335
1.28e-69
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83B; N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83B (FAM83B). Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. The N-terminus of FAM83B shows high homology to other FAM83 family members, indicating that FAM83B might have arisen early in vertebrate evolution by duplication of a gene in the FAM83 family.
Pssm-ID: 197279 Cd Length: 266 Bit Score: 229.72 E-value: 1.28e-69
N-terminal phospholipase D-like domain of the protein, Family with sequence similarity 83D; ...
88-335
3.53e-59
N-terminal phospholipase D-like domain of the protein, Family with sequence similarity 83D; N-terminal phospholipase D (PLD)-like domain of the protein Family with sequence similarity 83D (FAM83D), also known as spindle protein CHICA. CHICA is a cell-cycle-regulated spindle component, which localizes to the mitotic spindle and is both upregulated and phosphorylated during mitosis. CHICA is required to localize the chromokinesin Kid to the mitotic spindle and serves as a novel interaction partner of Kid, which is required for the generation of polar ejection forces and chromosome congression. Since the N-terminal PLD-like domain of FAM83D shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83D may share a similar three-dimensional fold with PLD enzymes, but is unlikely to carry PLD activity.
Pssm-ID: 197281 Cd Length: 271 Bit Score: 202.02 E-value: 3.53e-59
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence ...
86-335
1.28e-56
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83H; N-terminal phospholipase D (PLD)-like domain of the protein, Family with sequence similarity 83H (FAM83H) on chromosome 8q24.3, which localizes in the intracellular environment and is associated with vesicles, can be regulated by kinases, and plays important roles during ameloblast differentiation and enamel matrix calcification. The gene encoding protein FAM83H is the first gene involved in the etiology of amelogenesis imperfecta (AI), that encodes a non-secreted protein due to the absence of a signal peptide. Defects in gene FAM83H cause autosomal dominant hypocalcified amelogenesis imperfecta (ADHCAI). Since the N-terminal PLD-like domain of FAM83H shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83H may share a similar three-dimensional fold with PLD enzymes, but is most unlikely to carry PLD activity.
Pssm-ID: 197284 Cd Length: 265 Bit Score: 194.69 E-value: 1.28e-56
N-terminal phospholipase D-like domain of the uncharacterized protein Family with sequence ...
87-335
6.62e-52
N-terminal phospholipase D-like domain of the uncharacterized protein Family with sequence similarity 83G; N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83G (FAM83G). Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. The N-terminus of FAM83G shows high homology to other FAM83 family members, indicating that FAM83G might have arisen early in vertebrate evolution by duplication of a gene in the FAM83 family.
Pssm-ID: 197283 Cd Length: 275 Bit Score: 181.98 E-value: 6.62e-52
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence ...
87-335
1.53e-51
N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83F; N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83F (FAM83F). Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. The N-terminus of FAM83F shows high homology to other FAM83 family members, indicating that FAM83F might have arisen early in vertebrate evolution by duplication of a gene in the FAM83 family.
Pssm-ID: 197282 Cd Length: 268 Bit Score: 180.86 E-value: 1.53e-51
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar ...
186-331
6.51e-07
Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), and similar proteins. Nuc is an endonuclease from Salmonella typhimurium and the smallest known member of the PLD superfamily. It cleaves both single- and double-stranded DNA. PLD6 selectively hydrolyzes the terminal phosphodiester bond of phosphatidylcholine (PC), with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLD6 also catalyzes the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Both Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved sequence motif, the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which is essential for catalysis. PLDs utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. This subfamily also includes some uncharacterized hypothetical proteins, which have two HKD motifs in a single polypeptide chain.
Pssm-ID: 197215 [Multi-domain] Cd Length: 138 Bit Score: 49.22 E-value: 6.51e-07
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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