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A glycerophosphoethanolamine ethanolaminephosphodiesterase (GPE-EP) from Streptomyces sanglieri hydrolyzes glycerophosphoethanolamine to phosphoethanolamine and glycerol. The structure of GPE-EP was determined by the molecular replacement method using a search model generated with AlphaFold2. This structure includes the entire length of the mature protein and it is composed of an N-terminal domain and a novel C-terminal domain connected to a flexible linker. The N-terminal domain is the catalytic domain containing calcium ions at the catalytic site. Coordination bonds were observed between five amino acid residues and glycerol. Although the function of the C-terminal domain is currently unknown, inter-domain interactions between the N- and C-terminal domains may contribute to its relatively high thermostability., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Sphingomyelinase C (SMC) hydrolyzes sphingomyelin to ceramide and phosphocholine. Prokaryotic SMCs share sequence homology with mammalian SMCs that have enzymatic pH optima at neutral pH. SMC from the nonpathogenic prokaryote Streptomyces griseocarneus shows notable enzymatic features such as higher optimum pH and thermostability than other prokaryotic SMCs. Determination of the three-dimensional structure of S. griseocarneus-SMC (Sg-SMC) and comparison with other SMC structures represents a promising strategy to elucidate the unique enzymatic features of Sg-SMC on a structural basis. Therefore, we determined the crystal structure of Sg-SMC at 2.0 Å resolution by X-ray crystallography. Comparison of the Sg-SMC structure with three other structurally known SMCs from Listeria ivanovii, Bacillus cereus, and Staphylococcus aureus indicated that Sg-SMC is more diverse in sequence and that structural differences in the main chain between these SMCs are primarily located on the molecular surface distant from the active site. Comparison of the surface area of the four SMCs revealed that Sg-SMC has the most compact structure, which may contribute to the enhanced thermostability of Sg-SMC. Regarding the hydrogen bond network in the active site of Sg-SMC, a basic amino acid, Arg278, is involved, whereas the corresponding residue in other SMCs (Ser or Asn) does not form hydrogen bonds with metal-coordinating water molecules. Hydrogen bond formation between Arg278 and a Mg 2+ ion-coordinating water molecule may be responsible for the higher optimal pH of Sg-SMC compared to that of other SMCs., (Copyright © 2020 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.)

Objectives: To obtain an ethanolamine plasmalogen (PlsEtn)-hydrolyzing enzyme and to develop an assay that would help determine PlsEtn concentrations in human serum as an indicator of Alzheimer-type dementia and of arteriosclerosis., Results: Phospholipase A1s, SaPLA1 and SvPLA1 from, respectively, Streptomyces albidoflavus NA297 and S. avermitilis JCM5070-but not phospholipase B from Streptomyces sp. NA684, PLA2-Nagase from S. avermitilis, PLA2IIL from S. violaceoruber nor LIPOMOD 699L (porcine phospholipase)-hydrolyzed choline plasmalogen (PlsCho) and PlsEtn (PlsCho preferred over PlsEtn). Using a combination of SaPLA1, lysoplasmalogen-specific phospholipase D (LyPls-PLD), with amine oxidase, an end-point assay was developed for measuring serum PlsEtn concentration. The standard curve, generated using various amounts of PlsEtn in this assay, was linear between 0 and 0.2 mM. PlsEtn concentrations in forty-seven serum samples, determined independently by this enzyme-based assay and (125)I-HPLC method, exhibited a linear relationship, indicating that the assay is suitable for fast and accurate measurement of serum PlsEtn concentration., Conclusions: An assay, developed using SaPLA1, LyPls-PLD, and AOX, selectively measured PlsEtn levels in blood samples. This assay could be a useful diagnostic tool for early stage detection of diseases such as Alzheimer-type dementia and arteriosclerosis.

Streptomyces sanglieri extracellularly produces a glycerophosphoethanolamine ethanolaminephosphodiesterase (GPE-EP). The gene encoding the enzyme was found to consist of a 2124-bp ORF, which codes for an N-terminal 48 residue signal peptide required for secretion and a 660 amino acid mature protein with a calculated molecular mass of 72,918 Da. The maximum activity for sn-glycero-3-phosphoethanolamine (GPE) was found at pH 8.4 and 65°C in the presence of 0.1% (w/v) Triton X-100. The enzyme was activated in the presence of 2 mM EDTA; however, Zn(2+) remarkably inhibited activity. During the hydrolysis of GPE at 65°C and pH 8.4, the apparent Vmax, turnover number (kcat) and Km were determined to be 0.430 mmol min(-1) mg-protein(-1), 522 s(-1) and 0.785 mM, respectively. The enzyme exhibited specificity toward GPE and hydrolyzed ethanolamine-type substrates such as 1,2-dihexanoyl-sn-glycero-3-phosphoethanolamine, lysophosphatidylethanolamine and ethanolamine lysoplasmalogen, but not 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine. Moreover, the enzyme showed no activity toward other phospholipids, such as glycerophospholipids and plasmalogens, and sn-glycero-3-phosphodiesters except for sn-glycero-3-phosphoglycerol, suggesting that GPE-EP is not a phospholipase C (PLC). However, the amino acid sequence of GPE-EP shows 86% identity to that of PLC from Streptomyces sp. SirexAA-E (UniProt accession no. G2NFN1). Recombinant GPE-EP was functionally expressed in Escherichia coli using pET-24a(+). GPE hydrolysis by GPE-EP may represent a new pathway for phosphatidylethanolamine metabolism., (Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.)

A novel metal ion-independent glycerophosphocholine cholinephosphodiesterase (GPC-CP) of Streptomyces sanglieri was purified 53-fold from culture supernatant with 1.1% recovery (583 U/mg-protein). The enzyme functions as a monomer with a molecular mass of 66 kDa. The gene encoding the enzyme consists of a 1941-bp ORF that produces a signal peptide of 38 amino acids for secretion and a 646 amino acid mature protein with a calculated molecular mass of 70,447 Da. The maximum activity was found at pH 7.2 and 40°C. The enzyme hydrolyzed glycerol-3-phosphocholine (GPC) over a broad temperature range (37-60°C) and within a narrow pH range near pH 7. The enzyme was stable at 50°C for 30 min and between pH 5-10.5. The enzyme exhibited specificity toward GPC and glycerol-3-phosphoethanolamine and hydrolyzed glycerol-3-phosphate and lysophosphatidylcholine. However, the enzyme showed no activity toward any diacylglycerophospholipids and little activity toward other glycerol-3-phosphodiesters and lysophospholipids. The enzyme was not inhibited in the presence of 2 mM SDS and Mg(2+); however, Cu(2+), Zn(2+), and Co(2+) remarkably inhibited activity. Enzyme activity was also slightly enhanced by Ca(2+), Na(+), EDTA, DTT, and 2-mercaptoethanol. During the hydrolysis of GPC at 37°C and pH 7.2, apparent Vmax and turnover number (kcat) were determined to be 24.7 μmol min(-1) mg-protein(-1) and 29.0 s(-1), respectively. The apparent Km and kcat/Km values were 1.41 mM and 20.6 mM(-1) s(-1), respectively. GPC hydrolysis by GPC-CP might represent a new metabolic pathway for acquisition of a phosphorus source in actinomycetes., (Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.)

A novel metal ion-independent phospholipase B (PLB₆₈₄) from Streptomyces sp. strain NA684 was purified 264-fold from the culture supernatant with 2.85% recovery (6330 U·mg protein⁻¹). The enzyme functions as a monomer with a molecular mass of 38.9 kDa. Maximum activity was found at pH 8.4 and 50 °C. The substrate specificity was in the order: phosphatidylcholine ≥ phosphatidic acid ≥ lysophosphatidylcholine > phosphatidylserine > phosphatidylinositol > phosphatidylglycerol. The enzyme did not hydrolyze phosphatidylethanolamine, tristearin and dipalmitin. PLB₆₈₄ hydrolyzed lysophosphatidylcholine and diacylphosphatidylcholine, and lysophosphatidylcholine was primarily produced during the early stages of phosphatidylcholine hydrolysis. The apparent K(m), V(max) and k(cat) for hydrolysis of dimyristoyl phosphatidic acid were 14.5 mm, 15.8 mmol·min⁻¹·mg protein⁻¹ and 1.02 × 10⁴ s⁻¹, respectively. The positional specificity of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine hydrolysis was investigated using GC. In the reaction equilibrium, the molar ratio of released fatty acids (sn-1: sn-2) was 45 : 55. The ORF of the gene is 1239 bp in length and codes for a 30-amino acid signal peptide and a 382-amino acid mature enzyme. The deduced amino acid sequence of PLB₆₈₄ shows 60% identity to a uncharacterized protein of Streptomyces auratus AGR0001(UniProt accession number: J1RQY0). The extracellular production of PLB₆₈₄ was achieved using a pUC702 expression vector and Streptomyces lividans as the host. Mutagenesis analysis showed that Ser12 is essential for the catalytic function of PLB₆₈₄ and that the active site may include residues Ser330 and His332., (© 2013 FEBS.)

The metal-independent lipase from Streptomyces albidoflavus NA297 (SaPLA1) is a phospholipase A1 as it preferentially hydrolyzes the sn-1 acyl ester in glycerophospholipids, yielding a fatty acid and 2-acyl-lysophospholipid. The molecular mechanism underlying the substrate binding by SaPLA1 is currently unknown. In this study, the crystal structure of SaPLA1 was determined at 1.75Å resolutions by molecular replacement. A structural similarity search indicated the highest structural similarity to an esterase from Streptomyces scabies, followed by GDSL family enzymes. The SaPLA1 active site is composed of a Ser-His dyad (Ser11 and His218), whereby stabilization of the imidazole is provided by the main-chain carbonyl oxygen of Ser216, a common variation of the catalytic triad in many serine hydrolases, where this carbonyl maintains the orientation of the active site histidine residue. The hydrophobic pocket and cleft for lipid binding are adjacent to the active site, and are approximately 13-15Å deep and 14-16Å long. A partial polyethylene glycol structure was found in this hydrophobic pocket., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Sphingomyelinase C (SMC) of the actinomycete, Streptomycesgriseocarneus NBRC13471, was constitutively expressed to high levels using Streptomyces lividans host and thereafter was extracellularly secreted into the cell culture. Purified SMC had a high specific activity (approximately 550-950 U/mg) and was obtained in high yields (approximately 120 mg/L of culture). SMC activity was enhanced by MgCl(2), and the maximum activity (542±25 U/mg) was observed in the presence of 1.5 mol/L (M) MgCl(2). Dynamic light scattering analysis proved that the highest specific SMC activity was obtained with the smallest mixed micelles of sphingomyelin (SM) and Triton X-100. The turnover rate (k(cat)), K(m) and k(cat)/K(m) values for SM were 346 s(-1), 0.458 mM, and 756 mM(-1)s(-1), respectively, in the presence of 1M MgCl(2). The k(cat) was strongly influenced by the MgCl(2) concentration. By contrast, the K(m) value was independent of the MgCl(2) concentration and was almost constant. Circular dichroism spectroscopy indicated that MgCl(2) did not cause local structural changes in SMC. From these results, we concluded that the SMC activity enhancement by MgCl(2) was caused by the increased specific surface area of the mixed micelles composed of substrate, SM, and Triton X-100., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The metal-independent lipase from Streptomyces albidoflavus NA297 (SaPLA1) is a phospholipase A1 as it preferentially hydrolyzes the sn-1 acyl ester in glycerophospholipids, yielding a fatty acid and 2-acyl-lysophospholipid. The molecular mechanism underlying the substrate binding by SaPLA1 is currently unknown. In this study, the crystal structure of SaPLA1 was determined at 1.75Å resolutions by molecular replacement. A structural similarity search indicated the highest structural similarity to an esterase from Streptomyces scabies, followed by GDSL family enzymes. The SaPLA1 active site is composed of a Ser-His dyad (Ser11 and His218), whereby stabilization of the imidazole is provided by the main-chain carbonyl oxygen of Ser216, a common variation of the catalytic triad in many serine hydrolases, where this carbonyl maintains the orientation of the active site histidine residue. The hydrophobic pocket and cleft for lipid binding are adjacent to the active site, and are approximately 13–15Å deep and 14–16Å long. A partial polyethylene glycol structure was found in this hydrophobic pocket. [ABSTRACT FROM AUTHOR]

Abstract: Sphingomyelinase C (SMC) of the actinomycete, Streptomyces griseocarneus NBRC13471, was constitutively expressed to high levels using Streptomyces lividans host and thereafter was extracellularly secreted into the cell culture. Purified SMC had a high specific activity (approximately 550–950U/mg) and was obtained in high yields (approximately 120mg/L of culture). SMC activity was enhanced by MgCl2, and the maximum activity (542±25U/mg) was observed in the presence of 1.5mol/L (M) MgCl2. Dynamic light scattering analysis proved that the highest specific SMC activity was obtained with the smallest mixed micelles of sphingomyelin (SM) and Triton X-100. The turnover rate (k cat), K m and k cat/K m values for SM were 346s−1, 0.458mM, and 756mM−1 s−1, respectively, in the presence of 1M MgCl2. The k cat was strongly influenced by the MgCl2 concentration. By contrast, the K m value was independent of the MgCl2 concentration and was almost constant. Circular dichroism spectroscopy indicated that MgCl2 did not cause local structural changes in SMC. From these results, we concluded that the SMC activity enhancement by MgCl2 was caused by the increased specific surface area of the mixed micelles composed of substrate, SM, and Triton X-100. [Copyright &y& Elsevier]