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DeYonker NJ, Webster CE. Phosphoryl transfers of the phospholipase D superfamily: a quantum mechanical theoretical study. J Am Chem Soc 2013; 135:13764-74. [PMID: 24007383 DOI: 10.1021/ja4042753] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The HKD-containing Phospholipase D superfamily catalyzes the cleavage of the headgroup of phosphatidylcholine to produce phosphatidic acid and choline. The mechanism of this cleavage process is studied theoretically. The geometric basis of our models is the X-ray crystal structure of the five-coordinate phosphohistidine intermediate from Streptomyces sp . Strain PMF (PDB Code = 1V0Y ). Hybrid ONIOM QM:QM methodology with Density Functional Theory (DFT) and semiempirical PM6 (DFT:PM6) is used to acquire thermodynamic and kinetic data for the initial phosphoryl transfer, subsequent hydrolysis, and finally, the formation of the experimentally observed ″dead-end″ phosphohistidine product (PDB Code = 1V0W ). The model contains nineteen amino acid residues (including the two highly conserved HKD-motifs), four explicit water molecules, and the substrate. Via computations, the persistence of the short-lived five-coordinate phosphorane intermediate on the minutes times scale is rationalized. This five-coordinate phosphohistidine intermediate energetically exists between the hydrolysis event and ″substrate reorganization″ (the reorganization of the in vitro model substrate within the active site). Computations directly support the thermodynamic favorability of the in vitro four-coordinate phosphohistidine product. In vivo, the activation energy of substrate reorganization is too high, perhaps due to a combination of substrate immobility when embedded in the lipid bilayer, as well as its larger steric bulk compared to the compound used in the in vitro substrate soaks. On this longer time scale, the enzyme will migrate along the lipid membrane toward its next substrate target, rather than promote the formation of the dead-end product.
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Affiliation(s)
- Nathan J DeYonker
- The Department of Chemistry, The University of Memphis , 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
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Matsumoto Y, Mineta S, Murayama K, Sugimori D. A novel phospholipase B fromStreptomycessp. NA684 - purification, characterization, gene cloning, extracellular production and prediction of the catalytic residues. FEBS J 2013; 280:3780-96. [DOI: 10.1111/febs.12366] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/24/2013] [Accepted: 05/21/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Yusaku Matsumoto
- Department of Symbiotic Systems Science and Technology; Graduate School of Symbiotic Systems Science and Technology; Fukushima University; Japan
| | - Shingo Mineta
- Department of Symbiotic Systems Science and Technology; Graduate School of Symbiotic Systems Science and Technology; Fukushima University; Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics; Graduate School of Biomedical Engineering; Tohoku University; Sendai Japan
| | - Daisuke Sugimori
- Department of Symbiotic Systems Science and Technology; Graduate School of Symbiotic Systems Science and Technology; Fukushima University; Japan
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Phospholipase D as a catalyst: application in phospholipid synthesis, molecular structure and protein engineering. J Biosci Bioeng 2013; 116:271-80. [PMID: 23639419 DOI: 10.1016/j.jbiosc.2013.03.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 12/21/2022]
Abstract
Phospholipase D (PLD) is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids (PLs). Many reports exist on PLD-mediated synthesis of natural and tailor-made PLs with functional head groups, from easily available lecithin or phosphatidylcholine. Early studies on PLD-mediated synthesis mainly employed enzymes of plant origin, which were later supplanted by ones from microorganisms, especially actinomycetes. Many PLDs are members of the PLD superfamily, having one or two copies of a signature sequence, HxKxxxxD or HKD motif, in the primary structures. PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism. The catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base. PLD is being engineered to improve its activity and stability, alter head group specificity and further identify catalytically important residues. Since the knowledge on PLD enzymology is constantly expanding, this review focuses on recent advances in the field, regarding PLD-catalyzed synthesis of bioactive PLs, deeper understanding of substrate recognition and binding mechanism, altering substrate specificity, and improving thermostability. We introduced some of our recent results in combination with existing facts to further deepen the story on the nature of this useful enzyme.
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Effect of mixed-phospholipid layer on phospholipase D reaction-induced vesicle rupture. J Membr Biol 2012; 245:691-6. [PMID: 22622287 DOI: 10.1007/s00232-012-9438-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Accepted: 04/17/2012] [Indexed: 10/28/2022]
Abstract
Spherical phospholipid bilayers, or vesicles, were prepared layer by layer using a double-emulsion technique, which allows the outer layer of the vesicles to be formed with two phospholipids that have different head groups: phosphatidylcholine (PC) and phosphatidylethanolamine. At the outer layer of the vesicles, the phospholipase D (PLD) catalyzed for the conversion of PC to phosphatidic acid. The reaction caused by PLD induced the curvature change of the vesicles, which eventually led to the rupture of the vesicles. Before the investigation, the ratio of dioleoylphosphatidylethanolamine to oleoylhydroxyphosphatidylethanolamine was found as a condition such that the vesicles made with the mixed lipids were as stable as those made with pure dioleoylphosphatidylcholine. Response time from the PLD injection to vesicle rupture was monitored by the composition of the outer layer by the fluorescence intensity change of pH-sensitive dye encapsulated in the vesicles. The response time began to be slowed at approximately 30 % PC. The response times for the compositions were associated with the surface density of PC at the outer layer. These results also seem to be determined by the size of PLD, specifically the PLD active site.
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Rodriguez-Cerdeira C, Sanchez-Blanco E, Molares-Vila A, Alba A. Unveiling New Molecular Factors Useful for Detection of Pelvic Inflammatory Disease due to Chlamydia trachomatis Infection. ISRN OBSTETRICS AND GYNECOLOGY 2012; 2012:581725. [PMID: 23097713 PMCID: PMC3477744 DOI: 10.5402/2012/581725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Accepted: 08/31/2012] [Indexed: 11/23/2022]
Abstract
Background. Untreated Chlamydia trachomatis infections in women can result in disease sequelae such as pelvic inflammatory disease (PID), ultimately culminating in tubal occlusion and infertility. While nucleic acid amplification tests can effectively diagnose uncomplicated lower genital tract infections, they are not suitable for diagnosing upper genital tract pathological sequelae. Objective. The purpose of this paper was to provide a comprehensive review of new molecular factors associated with the diagnosis and prognosis of PID. Material and Methods. The literature was searched using the key words “Chlamydia trachomatis infections,” “pelvic inflammatory disease,” and “molecular factors” in the PubMed database. Relevant articles published between 1996 and 2012 were evaluated. Conclusions. The use of new molecular factors could potentially facilitate earlier diagnosis and prognosis in women with PID due to C. trachomatis infection.
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Nishimasu H, Ishizu H, Saito K, Fukuhara S, Kamatani MK, Bonnefond L, Matsumoto N, Nishizawa T, Nakanaga K, Aoki J, Ishitani R, Siomi H, Siomi MC, Nureki O. Structure and function of Zucchini endoribonuclease in piRNA biogenesis. Nature 2012; 491:284-7. [DOI: 10.1038/nature11509] [Citation(s) in RCA: 257] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/14/2012] [Indexed: 11/09/2022]
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Phase effect of mixed-phospholipid layer on phospholipase D reaction-induced-vesicle rupture. Colloids Surf B Biointerfaces 2012; 97:207-10. [DOI: 10.1016/j.colsurfb.2012.04.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 04/13/2012] [Accepted: 04/21/2012] [Indexed: 11/18/2022]
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Structure-function studies of a plant tyrosyl-DNA phosphodiesterase provide novel insights into DNA repair mechanisms of Arabidopsis thaliana. Biochem J 2012; 443:49-56. [PMID: 22214184 PMCID: PMC3304491 DOI: 10.1042/bj20111308] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
TDP1 (tyrosyl-DNA phosphodiesterase 1), a member of the PLD (phospholipase D) superfamily, catalyses the hydrolysis of a phosphodiester bond between a tyrosine residue and the 3′-phosphate of DNA. We have previously identified and characterized the AtTDP gene in Arabidopsis thaliana, an orthologue of yeast and human TDP1 genes. Sequence alignment of TDP1 orthologues revealed that AtTDP has both a conserved C-terminal TDP domain and, uniquely, an N-terminal SMAD/FHA (forkhead-associated) domain. To help understand the function of this novel enzyme, we analysed the substrate saturation kinetics of full-length AtTDP compared with a truncated AtTDP mutant lacking the N-terminal FHA domain. The recombinant AtTDP protein hydrolysed a single-stranded DNA substrate with Km and kcat/Km values of 703±137 nM and (1.5±0.04)×109M−1·min−1 respectively. The AtTDP-(Δ1–122) protein (TDP domain) showed kinetic parameters that were equivalent to those of the full-length AtTDP protein. A basic amino acid sequence (RKKVKP) within the AtTDP-(Δ123–605) protein (FHA domain) was necessary for nuclear localization of AtTDP. Analysis of active-site mutations showed that a histidine and a lysine residue in each of the HKD motifs were critical for enzyme activity. Vanadates, inhibitors of phosphoryl transfer reactions, inhibited AtTDP enzymatic activity and retarded the growth of an Arabidopsis tdp mutant. Finally, we showed that expression of the AtTDP gene could complement a yeast tdp1Δrad1Δ mutant, rescuing the growth inhibitory effects of vanadate analogues and CPT (camptothecin). Taken together, the results of the present study demonstrate the structure-based function of AtTDP through which AtTDP can repair DNA strand breaks in plants.
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Abstract
Phospholipids are present in all living organisms. They are a major component of all biological membranes, along with glycolipids and cholesterol. Enzymes aimed at cleaving the various bonds in phospholipids, namely phospholipases, are consequently widespread in nature, playing very diverse roles from aggression in snake venom to signal transduction, lipid mediators production, and digestion in humans. Although all phospholipases target phospholipids as substrates, they vary in the site of action on the phospholipids molecules, physiological function, mode of action, and their regulation. Significant studies on phospholipases characterization, physiological role, and industrial potential have been conducted worldwide. Some of them have been directed for biotechnological advances, such as gene discovery and functional enhancement by protein engineering. Others reported phospholipases as virulence factors and major causes of pathophysiological effects. In this introductory chapter, we provide brief details of different phospholipases.
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Affiliation(s)
- Ahmed Aloulou
- National School of Engineers of Sfax, University of Sfax, Sfax, Tunisia.
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60
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Jang YH, Min DS. Intermolecular association between caspase-mediated cleavage fragments of phospholipase D1 protects against apoptosis. Int J Biochem Cell Biol 2011; 44:358-65. [PMID: 22108201 DOI: 10.1016/j.biocel.2011.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 10/24/2011] [Accepted: 11/07/2011] [Indexed: 11/17/2022]
Abstract
Phospholipase D plays an anti-apoptotic role but little is known about dynamics of phospholipase D turnover during apoptosis. We have recently identified phospholipase D1 as a new substrate of caspases which generates the N-terminal and C-terminal fragment of phospholipase D1. In the present study, we tried to investigate whether association of the caspase cleavage fragments may be involved in regulation of apoptosis. Ectopically expressed C-terminal fragment, but not N-terminal fragment of phospholipase D1, is exclusively imported into the nucleus via a nuclear localization sequence; however, endogenous C-terminal fragment of phospholipase D1 from etoposide-induced apoptotic cells and Alzheimer's disease brain tissues with active caspase-3, was localized in the cytosolic fraction as well as the nuclear fraction. Intermolecular association between the two fragments of phospholipase D1 through hydrophobic residues within the catalytic motif inhibited nuclear localization of C-terminal fragment of phospholipase D1, and two catalytic motif and nuclear localization sequence regulated nuclocytoplasmic shuttling of phospholipase D1. Moreover, hydrophobic residues involved in the intermolecular association are also required for both its enzymatic activity and anti-apoptotic function. Taken together, we demonstrate that interdomain association and dissociation of phospholipase D1 might provide new insights into modulation of apoptosis.
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Affiliation(s)
- Young Hoon Jang
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 609-735, Republic of Korea
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61
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Selvy PE, Lavieri RR, Lindsley CW, Brown HA. Phospholipase D: enzymology, functionality, and chemical modulation. Chem Rev 2011; 111:6064-119. [PMID: 21936578 PMCID: PMC3233269 DOI: 10.1021/cr200296t] [Citation(s) in RCA: 267] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paige E Selvy
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37064, USA
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Abdelkafi S, Abousalham A. Kinetic study of sunflower phospholipase Dα: interactions with micellar substrate, detergents and metals. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:752-757. [PMID: 21353787 DOI: 10.1016/j.plaphy.2011.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 02/02/2011] [Indexed: 05/30/2023]
Abstract
Phospholipase Dα (PLDα) purified from six-day post-germinated sunflower seeds was inactive in vitro on bilamellar substrates. It was fully active on mixed micelles made with phospholipids and a mixture of Triton-X100 and SDS at equal concentrations. It had an absolute need for divalent ions and calcium ions at millimolar concentration were the most efficient. Calcium had two effects. Firstly, using the fluorescent probe 2-p-toluidinylnaphtalene-6-sulfonate, we showed that the enzyme was able to bind calcium with a dissociation constant of 40-50 mM. This high value is probably due to the modification of the C2 domain which lacks some coordination residues allowing the binding of the metal. Secondly, using turbidity measurements, we showed that the metal ions interact with the SDS contained in the mixed micelles thus leading to an aggregated form of the substrate which is more easily hydrolyzed by PLDα.
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Affiliation(s)
- Slim Abdelkafi
- Organization and Dynamics of Biological Membranes, UMR 5246 ICBMS, CNRS-Université Claude Bernard Lyon 1, Bâtiment Raulin, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, Cedex, France
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63
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Collet T, Macnaughton T, Walsh T, Debattista J, Timms P. Identification of novel markers for uncomplicated lower genital tract infections and upper genital tract pathology due to Chlamydia trachomatis. Int J Infect Dis 2011; 15:e257-66. [DOI: 10.1016/j.ijid.2010.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 11/19/2010] [Accepted: 12/19/2010] [Indexed: 10/18/2022] Open
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Yoshikawa F, Banno Y, Otani Y, Yamaguchi Y, Nagakura-Takagi Y, Morita N, Sato Y, Saruta C, Nishibe H, Sadakata T, Shinoda Y, Hayashi K, Mishima Y, Baba H, Furuichi T. Phospholipase D family member 4, a transmembrane glycoprotein with no phospholipase D activity, expression in spleen and early postnatal microglia. PLoS One 2010; 5:e13932. [PMID: 21085684 PMCID: PMC2978679 DOI: 10.1371/journal.pone.0013932] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 10/22/2010] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Phospholipase D (PLD) catalyzes conversion of phosphatidylcholine into choline and phosphatidic acid, leading to a variety of intracellular signal transduction events. Two classical PLDs, PLD1 and PLD2, contain phosphatidylinositide-binding PX and PH domains and two conserved His-x-Lys-(x)(4)-Asp (HKD) motifs, which are critical for PLD activity. PLD4 officially belongs to the PLD family, because it possesses two HKD motifs. However, it lacks PX and PH domains and has a putative transmembrane domain instead. Nevertheless, little is known regarding expression, structure, and function of PLD4. METHODOLOGY/PRINCIPAL FINDINGS PLD4 was analyzed in terms of expression, structure, and function. Expression was analyzed in developing mouse brains and non-neuronal tissues using microarray, in situ hybridization, immunohistochemistry, and immunocytochemistry. Structure was evaluated using bioinformatics analysis of protein domains, biochemical analyses of transmembrane property, and enzymatic deglycosylation. PLD activity was examined by choline release and transphosphatidylation assays. Results demonstrated low to modest, but characteristic, PLD4 mRNA expression in a subset of cells preferentially localized around white matter regions, including the corpus callosum and cerebellar white matter, during the first postnatal week. These PLD4 mRNA-expressing cells were identified as Iba1-positive microglia. In non-neuronal tissues, PLD4 mRNA expression was widespread, but predominantly distributed in the spleen. Intense PLD4 expression was detected around the marginal zone of the splenic red pulp, and splenic PLD4 protein recovered from subcellular membrane fractions was highly N-glycosylated. PLD4 was heterologously expressed in cell lines and localized in the endoplasmic reticulum and Golgi apparatus. Moreover, heterologously expressed PLD4 proteins did not exhibit PLD enzymatic activity. CONCLUSIONS/SIGNIFICANCE Results showed that PLD4 is a non-PLD, HKD motif-carrying, transmembrane glycoprotein localized in the endoplasmic reticulum and Golgi apparatus. The spatiotemporally restricted expression patterns suggested that PLD4 might play a role in common function(s) among microglia during early postnatal brain development and splenic marginal zone cells.
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Affiliation(s)
- Fumio Yoshikawa
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Yoshiko Banno
- Department of Cell Signaling, Gifu University Graduate School of Medicine, Gifu, Gifu, Japan
| | - Yoshinori Otani
- Department of Molecular Neurobiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Yoshihide Yamaguchi
- Department of Molecular Neurobiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Yuko Nagakura-Takagi
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Noriyuki Morita
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
- Yasuda Women's University, Hiroshima, Hiroshima, Japan
| | - Yumi Sato
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Chihiro Saruta
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Hirozumi Nishibe
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Tetsushi Sadakata
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
- JST, CREST, Kawaguchi, Saitama, Japan
| | - Yo Shinoda
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
- JST, CREST, Kawaguchi, Saitama, Japan
| | - Kanehiro Hayashi
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
- JST, CREST, Kawaguchi, Saitama, Japan
| | - Yuriko Mishima
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
- JST, CREST, Kawaguchi, Saitama, Japan
| | - Hiroko Baba
- Department of Molecular Neurobiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Teiichi Furuichi
- Laboratory for Molecular Neurogenesis, RIKEN Brain Science Institute, Wako, Saitama, Japan
- JST, CREST, Kawaguchi, Saitama, Japan
- Saitama University Graduate School of Science and Engineering, Saitama, Saitama, Japan
- Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Hiroshima, Japan
- * E-mail:
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Pleskot R, Potocký M, Pejchar P, Linek J, Bezvoda R, Martinec J, Valentová O, Novotná Z, Zárský V. Mutual regulation of plant phospholipase D and the actin cytoskeleton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:494-507. [PMID: 20149133 DOI: 10.1111/j.1365-313x.2010.04168.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Membrane lipids and cytoskeleton dynamics are intimately inter-connected in the eukaryotic cell; however, only recently have the molecular mechanisms operating at this interface in plant cells been addressed experimentally. Phospholipase D (PLD) and its product phosphatidic acid (PA) were discovered to be important regulators in the membrane-cytoskeleton interface in eukaryotes. Here we report the mechanistic details of plant PLD-actin interactions. Inhibition of PLD by n-butanol compromises pollen tube actin, and PA rescues the detrimental effect of n-butanol on F-actin, showing clearly the importance of the PLD-PA interaction for pollen tube F-actin dynamics. From various candidate tobacco PLDs isoforms, we identified NtPLDbeta1 as a regulatory partner of actin, by both activity and in vitro interaction assays. Similarly to published data, the activity of tobacco PIP(2)-dependent PLD (PLDbeta) is specifically enhanced by F-actin and inhibited by G-actin. We then identified the NtPLDbeta1 domain responsible for actin interactions. Using sequence- and structure-based analysis, together with site-directed mutagenesis, we identified Asn323 and Thr382 of NtPLDbeta1 as the crucial amino acids in the actin-interacting fold. The effect of antisense-mediated suppression of NtPLDbeta1 or NtPLDdelta on pollen tube F-actin dynamics shows that NtPLDbeta1 is the active partner in PLD-actin interplay. The positive feedback loop created by activation of PLDbeta by F-actin and of F-actin by PA provides an important mechanism to locally increase membrane-F-actin dynamics in the cortex of plant cells.
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Affiliation(s)
- Roman Pleskot
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, v.v.i., Rozvojová 263, 165 02 Prague 6, Czech Republic
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D'Arrigo P, Servi S. Synthesis of lysophospholipids. Molecules 2010; 15:1354-77. [PMID: 20335986 PMCID: PMC6257299 DOI: 10.3390/molecules15031354] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 03/04/2010] [Accepted: 03/05/2010] [Indexed: 12/01/2022] Open
Abstract
New synthetic methods for the preparation of biologically active phospholipids and lysophospholipids (LPLs) are very important in solving problems of membrane-chemistry and biochemistry. Traditionally considered just as second-messenger molecules regulating intracellular signalling pathways, LPLs have recently shown to be involved in many physiological and pathological processes such as inflammation, reproduction, angiogenesis, tumorogenesis, atherosclerosis and nervous system regulation. Elucidation of the mechanistic details involved in the enzymological, cell-biological and membrane-biophysical roles of LPLs relies obviously on the availability of structurally diverse compounds. A variety of chemical and enzymatic routes have been reported in the literature for the synthesis of LPLs: the enzymatic transformation of natural glycerophospholipids (GPLs) using regiospecific enzymes such as phospholipases A1 (PLA1), A2 (PLA2) phospholipase D (PLD) and different lipases, the coupling of enzymatic processes with chemical transformations, the complete chemical synthesis of LPLs starting from glycerol or derivatives. In this review, chemo-enzymatic procedures leading to 1- and 2-LPLs will be described.
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Affiliation(s)
- Paola D'Arrigo
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica Giulio Natta, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy. paola.d'
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Mander P, Simkhada JR, Cho SS, Park SJ, Choi HS, Lee HC, Sohng JK, Yoo JC. A novel Ca2+-dependent phospholipase D from Streptomyces tendae, possessing only hydrolytic activity. Arch Pharm Res 2009; 32:1461-7. [PMID: 19898811 DOI: 10.1007/s12272-009-2017-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 06/30/2009] [Accepted: 08/11/2009] [Indexed: 10/20/2022]
Abstract
An extracellular phospholipase D (PLD(St)) was purified from Streptomyces tendae by two successive chromatographic steps on Sepharose CL-6B and DEAE-Sepharose CL-6B. Molecular weight of the PLD(St) was estimated to be approximately 43 kDa by sodium dodecyl sulfatepolyacrylamide gel electrophoresis. Maximal activity was at pH 8 and 60 degrees C, and the enzyme was stable at or below 60 degrees C and between pH 8 and 10, when assayed after 1.5 and 24 h, respectively. The enzyme activity had an absolute requirement of Ca(2+), and the maximum activity was at 2 mM CaCl(2). The Km and Vmax values for phosphatidyl choline were 0.95 mM and 810 micromol min(-1) mg(-1), respectively. More importantly, PLD(St) could not catalyze transphosphatidylation of glycerol, L-serine, myo-inositol and ethanolamine, which have been extensively used to evaluate the activity. The result strongly suggests that PLD( St ) does not have the transphosphatidylation activity, thereby making it the first Streptomyces PLD possessing only hydrolytic activity. PLD(St) may therefore be a novel type of PLD enzyme.
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Affiliation(s)
- Poonam Mander
- Department of Pharmacy, College of Pharmacy, Chosun University, Gwangju, Korea
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Mansfeld J, Ulbrich-Hofmann R. Modulation of phospholipase D activity in vitro. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:913-26. [DOI: 10.1016/j.bbalip.2009.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 03/03/2009] [Accepted: 03/04/2009] [Indexed: 11/30/2022]
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Sandhya S, Rani SS, Pankaj B, Govind MK, Offmann B, Srinivasan N, Sowdhamini R. Length variations amongst protein domain superfamilies and consequences on structure and function. PLoS One 2009; 4:e4981. [PMID: 19333395 PMCID: PMC2659687 DOI: 10.1371/journal.pone.0004981] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Accepted: 02/26/2009] [Indexed: 11/24/2022] Open
Abstract
Background Related protein domains of a superfamily can be specified by proteins of diverse lengths. The structural and functional implications of indels in a domain scaffold have been examined. Methodology In this study, domain superfamilies with large length variations (more than 30% difference from average domain size, referred as ‘length-deviant’ superfamilies and ‘length-rigid’ domain superfamilies (<10% length difference from average domain size) were analyzed for the functional impact of such structural differences. Our delineated dataset, derived from an objective algorithm, enables us to address indel roles in the presence of peculiar structural repeats, functional variation, protein-protein interactions and to examine ‘domain contexts’ of proteins tolerant to large length variations. Amongst the top-10 length-deviant superfamilies analyzed, we found that 80% of length-deviant superfamilies possess distant internal structural repeats and nearly half of them acquired diverse biological functions. In general, length-deviant superfamilies have higher chance, than length-rigid superfamilies, to be engaged in internal structural repeats. We also found that ∼40% of length-deviant domains exist as multi-domain proteins involving interactions with domains from the same or other superfamilies. Indels, in diverse domain superfamilies, were found to participate in the accretion of structural and functional features amongst related domains. With specific examples, we discuss how indels are involved directly or indirectly in the generation of oligomerization interfaces, introduction of substrate specificity, regulation of protein function and stability. Conclusions Our data suggests a multitude of roles for indels that are specialized for domain members of different domain superfamilies. These specialist roles that we observe and trends in the extent of length variation could influence decision making in modeling of new superfamily members. Likewise, the observed limits of length variation, specific for each domain superfamily would be particularly relevant in the choice of alignment length search filters commonly applied in protein sequence analysis.
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Affiliation(s)
- Sankaran Sandhya
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India
| | - Saane Sudha Rani
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India
| | - Barah Pankaj
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India
| | | | - Bernard Offmann
- Laboratoire de Biochimie et Génétique Moléculaire BP 7151, Université de La Réunion, La Réunion, France
| | | | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India
- * E-mail:
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70
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Uesugi Y, Hatanaka T. Phospholipase D mechanism using Streptomyces PLD. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:962-9. [PMID: 19416643 DOI: 10.1016/j.bbalip.2009.01.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 01/19/2009] [Accepted: 01/28/2009] [Indexed: 11/17/2022]
Abstract
Phospholipase D (PLD) plays various roles in important biological processes and physiological functions, including cell signaling. Streptomyces PLDs show significant sequence similarity and belong to the PLD superfamily containing two catalytic HKD motifs. These PLDs have conserved catalytic regions and are among the smallest PLD enzymes. Therefore, Streptomyces PLDs are thought to be suitable models for studying the reaction mechanism among PLDs from other sources. Furthermore, Streptomyces PLDs present advantages related to their broad substrate specificity and ease of enzyme preparation. Moreover, the tertiary structure of PLD has been elucidated only for PLD from Streptomyces sp. PMF. This article presents a review of recently reported studies of the mechanism of the catalytic reaction, substrate recognition, substrate specificity and stability of Streptomyces PLD using various protein engineering methods and surface plasmon resonance analysis.
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Affiliation(s)
- Yoshiko Uesugi
- Research Institute for Biological Sciences (RIBS), Kaga-gun, Okayama, Japan
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71
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Dippe M, Ulbrich-Hofmann R. Substrate specificity in phospholipid transformations by plant phospholipase D isoenzymes. PHYTOCHEMISTRY 2009; 70:361-365. [PMID: 19251290 DOI: 10.1016/j.phytochem.2009.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 12/09/2008] [Accepted: 01/22/2009] [Indexed: 05/27/2023]
Abstract
Phospholipase D (PLD) catalyzes the hydrolysis and transesterification of glycerophospholipids at the terminal phosphodiester bond. In many plants, several isoforms of PLD have been identified without knowing their functional differences. In this paper, the specificities of two PLD isoenzymes from white cabbage (Brassica oleracea var. capitata) and two ones from opium poppy (Papaver somniferum L.), which were recombinantly produced in Escherichia coli, were compared in the hydrolysis of phospholipids with different head groups and in the transphosphatidylation of phosphatiylcholine with several acceptor alcohols. In a biphasic reaction system, consisting of buffer and diethyl ether, the highly homologous isoenzymes are able to hydrolyze phosphatidylcholine, -glycerol, -ethanolamine, -inositol and - with one exception - also phosphatidylserine but with different individual reaction rates. In transphosphatidylation of phosphatidylcholine, they show significant differences in the rates of head group exchange but with the same trend in the preference of acceptor alcohols (ethanolamine>glycerol>>l-serine). For l- and d-serine a stereoselectivity of PLD was observed. The results suggest a physiological relevance of the different hydrolytic and transphosphatidylation activities in plant PLD isoenzymes.
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Affiliation(s)
- Martin Dippe
- Institute of Biochemistry and Biotechnology, Martin-Luther University, Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06099 Halle, Germany
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72
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Zhang YN, Lu FP, Chen GQ, Li Y, Wang JL. Expression, purification, and characterization of phosphatidylserine synthase from Escherichia coli K12 in Bacillus subtilis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:122-126. [PMID: 19072541 DOI: 10.1021/jf802664u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Although phosphatidylserine synthase (PSS) from Escherichia coli is an ideal enzyme for phospholipid production, its application in the food industry has been limited because of the low PSS yield. In this study, the pss gene was cloned from E. coli K(12) and expressed in Bacillus subtilis DB104, and the recombinant PSS was characterized subsequently. PSS was purified to 39.59-fold, and the highest activity was detected as 13.62 U/mg. The enzyme was found to be stable in a pH range of 6.5-9.5, with optimal pH values of 8.0 for hydrolysis and 7.0 for transphosphatidylation, respectively. The optimal temperature for PSS activity was 35 degrees C. The enzyme activity could be detected after 1 h of heating at 65 degrees C. Among the detected detergents and metal ions, Triton X-100, Ca(2+), Mn(2+), and Co(2+) could improve PSS activity. The transformation of phosphatidylcholine to phosphatidylserine under PSS catalyzation was carried out in a biphasic system, which confirmed the actual catalyzing ability of the recombinant protein.
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Affiliation(s)
- Ye-Ni Zhang
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, 300457 Tianjin, People's Republic of China
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73
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Kuppe K, Kerth A, Blume A, Ulbrich-Hofmann R. Calcium-induced membrane microdomains trigger plant phospholipase D activity. Chembiochem 2009; 9:2853-9. [PMID: 18942690 DOI: 10.1002/cbic.200800431] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Plant alpha-type phospholipase D proteins are calcium-dependent, lipolytic enzymes. The morphology of the aggregates of their phospholipid substrate fundamentally defines the interaction between the enzyme and the surface. Here we demonstrate that the Ca(2+)-induced generation of membrane microdomains dramatically activates alpha-type phospholipase D from white cabbage. 500-fold stimulation was observed upon incorporation of 10 mol % 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphate (POPA) into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) vesicles in the presence of Ca(2+) ions. Enhanced association of PLDalpha2 with phospholipid surfaces containing anionic components was indicated by lag phase analysis and film balance measurements. Differential scanning calorimetry showed that the POPA-specific activation correlates with the phase behavior of the POPC/POPA vesicles in the presence of Ca(2+) ions. We conclude from the results that the Ca(2+)-induced formation of POPA microdomains is the crucial parameter that facilitates the binding of PLD to the phospholipid surface and suggest that this effect serves as a cellular switch for controlling PLD activity.
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Affiliation(s)
- Konstantin Kuppe
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes Strasse 3, 06120 Halle, Germany
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74
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Simkhada JR, Lee HJ, Jang SY, Cho SS, Park EJ, Sohng JK, Yoo JC. A novel alkalo- and thermostable phospholipase D from Streptomyces olivochromogenes. Biotechnol Lett 2008; 31:429-35. [PMID: 19039525 DOI: 10.1007/s10529-008-9890-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 10/28/2008] [Accepted: 11/11/2008] [Indexed: 10/21/2022]
Abstract
A 60 kDa phospholipase D (PLD) was obtained from Streptomyces olivochromogenes by one-step chromatography on Sepharose CL-6B. Maximal activity was at pH 8 and 75 degrees C and the enzyme was stable from pH 7 to 13 and from 55 to 75 degrees C. Thermal and pH stability with temperature optimum of the enzyme were highest among Streptomyces PLDs reported so far. The activity was Ca(2+)-dependent and enhanced by detergents. The Km and Vmax values for phosphatidylcholine were 0.6 mM and 650 mumol min(-1) mg(-1), respectively. In addition, the enzyme also revealed transphosphatidylation activity, which was optimum at pH 8 and 50 degrees C. The first 15 amino acid residues of the N terminal sequence were ADYTPGAPGIGDPYY, which are significantly different from the other known PLDs. The enzyme may therefore be a novel PLD with potential application in the lipid industry.
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Affiliation(s)
- Jaya Ram Simkhada
- Department of Pharmacy, College of Pharmacy, Chosun University, Gwangju, 501-759, South Korea
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75
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Dexheimer TS, Antony S, Marchand C, Pommier Y. Tyrosyl-DNA phosphodiesterase as a target for anticancer therapy. Anticancer Agents Med Chem 2008; 8:381-9. [PMID: 18473723 DOI: 10.2174/187152008784220357] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a recently discovered enzyme that catalyzes the hydrolysis of 3'-phosphotyrosyl bonds. Such linkages form in vivo following the DNA processing activity of topoisomerase I (Top1). For this reason, Tdp1 has been implicated in the repair of irreversible Top1-DNA covalent complexes, which can be generated by either exogenous or endogenous factors. Tdp1 has been regarded as a potential therapeutic co-target of Top1 in that it seemingly counteracts the effects of Top1 inhibitors, such as camptothecin and its clinically used derivatives. Thus, by reducing the repair of Top1-DNA lesions, Tdp1 inhibitors have the potential to augment the anticancer activity of Top1 inhibitors provided there is a presence of genetic abnormalities related to DNA checkpoint and repair pathways. Human Tdp1 can also hydrolyze other 3'-end DNA alterations including 3'-phosphoglycolates and 3'-abasic sites indicating it may function as a general 3'-DNA phosphodiesterase and repair enzyme. The importance of Tdp1 in humans is highlighted by the observation that a recessive mutation in the human TDP1 gene is responsible for the inherited disorder, spinocerebellar ataxia with axonal neuropathy (SCAN1). This review provides a summary of the biochemical and cellular processes performed by Tdp1 as well as the rationale behind the development of Tdp1 inhibitors for anticancer therapy.
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Affiliation(s)
- Thomas S Dexheimer
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892-4255, USA
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76
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Expression and purification of the D4 region of PLD1 and characterization of its interaction with PED-PEA15. Protein Expr Purif 2008; 59:302-8. [DOI: 10.1016/j.pep.2008.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 02/22/2008] [Accepted: 02/22/2008] [Indexed: 11/20/2022]
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77
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Cloning and expression of phospholipase D genepld fromStreptomyces chromofuscus. ANN MICROBIOL 2008. [DOI: 10.1007/bf03175321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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78
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Masayama A, Takahashi T, Tsukada K, Nishikawa S, Takahashi R, Adachi M, Koga K, Suzuki A, Yamane T, Nakano H, Iwasaki Y. Streptomyces Phospholipase D Mutants with Altered Substrate Specificity Capable of Phosphatidylinositol Synthesis. Chembiochem 2008; 9:974-81. [DOI: 10.1002/cbic.200700528] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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79
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Dippe M, Mrestani-Klaus C, Schierhorn A, Ulbrich-Hofmann R. Phospholipase D-catalyzed synthesis of new phospholipids with polar head groups. Chem Phys Lipids 2008; 152:71-7. [DOI: 10.1016/j.chemphyslip.2008.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 01/11/2008] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
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80
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Chan SH, Bao Y, Ciszak E, Laget S, Xu SY. Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities. Nucleic Acids Res 2007; 35:6238-48. [PMID: 17855396 PMCID: PMC2094064 DOI: 10.1093/nar/gkm665] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Creating endonucleases with novel sequence specificities provides more possibilities to manipulate DNA. We have created a chimeric endonuclease (CH-endonuclease) consisting of the DNA cleavage domain of BmrI restriction endonuclease and C.BclI, a controller protein of the BclI restriction-modification system. The purified chimeric endonuclease, BmrI198-C.BclI, cleaves DNA at specific sites in the vicinity of the recognition sequence of C.BclI. Double-strand (ds) breaks were observed at two sites: 8 bp upstream and 18 bp within the C-box sequence. Using DNA substrates with deletions of C-box sequence, we show that the chimeric endonuclease requires the 5' half of the C box only for specific cleavage. A schematic model is proposed for the mode of protein-DNA binding and DNA cleavage. The present study demonstrates that the BmrI cleavage domain can be used to create combinatorial endonucleases that cleave DNA at specific sequences dictated by the DNA-binding partner. The resulting endonucleases will be useful in vitro and in vivo to create ds breaks at specific sites and generate deletions.
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Affiliation(s)
| | | | | | | | - Shuang-yong Xu
- *To whom correspondence should be addressed. +1 978 380 7287+1 978 921 1350
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81
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Ogino C, Daido H, Ohmura Y, Takada N, Itou Y, Kondo A, Fukuda H, Shimizu N. Remarkable enhancement in PLD activity from Streptoverticillium cinnamoneum by substituting serine residue into the GG/GS motif. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:671-8. [PMID: 17499030 DOI: 10.1016/j.bbapap.2007.04.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 04/05/2007] [Accepted: 04/06/2007] [Indexed: 11/21/2022]
Abstract
The gene that encodes phospholipase D (PLD) from Streptoverticillium cinnamoneum contains three consensus regions (Region I, II and IV as shown in Fig. 1A) that are conserved among the PLD superfamily. The glycine-glycine (GG) motif in Region I and the glycine-serine (GS) motif in Region IV are also conserved in the PLD superfamily. These (GG and GS) motifs are located 7 residues downstream from each HKD motif. In an investigation of fifteen GG/GS motif mutants, generated as fusion proteins with maltose-binding protein (MBP-PLDs), three highly active mutants were identified. Three of the mutants (G215S, G216S, and G216S-S489G) contained a serine residue in the GG motif, and exhibited approximately a 9-27-fold increased transphosphatidylation activity to DPPC compared with recombinant wild type MBP-PLD. When heat stability was compared between three mutants and the recombinant wild type, only G216S-S489G showed heat labile properties. It appears that the 489th serine residue in the GS motif also contributes to the thermal stability of the enzyme. In addition, the GG/GS motif was very close to the active center residue, including two HKD motifs, as shown by computer modeling. The findings suggest that the GG/GS motif of PLD is a key motif that affects catalytic function and enzymatic stability.
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Affiliation(s)
- Chiaki Ogino
- The Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan.
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Abstract
Phospholipases D play an important role in the regulation of cellular processes in plants and mammals. Moreover, they are an essential tool in the synthesis of phospholipids and phospholipid analogs. Knowledge of phospholipase D structures, however, is widely restricted to sequence data. The only known tertiary structure of a microbial phospholipase D cannot be generalized to eukaryotic phospholipases D. In this study, the isoenzyme form of phospholipase D from white cabbage (PLDalpha2), which is the most widely used plant phospholipase D in biocatalytic applications, has been characterized by small-angle X-ray scattering, UV-absorption, CD and fluorescence spectroscopy to yield the first insights into its secondary and tertiary structure. The structural model derived from small-angle X-ray scattering measurements reveals a barrel-shaped monomer with loosely structured tops. The far-UV CD-spectroscopic data indicate the presence of alpha-helical as well as beta-structural elements, with the latter being dominant. The fluorescence and near-UV CD spectra point to tight packing of the aromatic residues in the core of the protein. From the near-UV CD signals and activity data as a function of the calcium ion concentration, two binding events characterized by dissociation constants in the ranges of 0.1 mm and 10-20 mm can be confirmed. The stability of PLDalpha2 proved to be substantially reduced in the presence of calcium ions, with salt-induced aggregation being the main reason for irreversible inactivation.
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Affiliation(s)
- Susanne Stumpe
- Martin-Luther University Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Halle, Saale, Germany
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83
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Schäfer P, Cymerman IA, Bujnicki JM, Meiss G. Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species. Protein Sci 2007; 16:82-91. [PMID: 17192590 PMCID: PMC2222834 DOI: 10.1110/ps.062535307] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Lysosomal DNase IIalpha is essential for DNA waste removal and auxiliary apoptotic DNA fragmentation in higher eukaryotes. Despite the key role of this enzyme, little is known about its structure-function relationships. Here, mutational and biochemical analyses were used to characterize human DNase IIalpha variants expressed in mammalian cells. The resulting data strongly support the hypothesis that the enzyme is a monomeric phospholipase D-family member with a pseudodimeric protein fold. According to our results, DNase IIalpha contains two requisite PLD-signature motifs ((113)HTK(115) and (295)HSK(297)) in the N- and C-terminal subdomains, respectively, that together form a single active site. Based on these data, we present an experimentally validated structural model of DNase IIalpha.
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Affiliation(s)
- Patrick Schäfer
- Institute of Biochemistry, Justus-Liebig-University Giessen, Germany
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84
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De Maria L, Vind J, Oxenbøll KM, Svendsen A, Patkar S. Phospholipases and their industrial applications. Appl Microbiol Biotechnol 2007; 74:290-300. [PMID: 17221199 DOI: 10.1007/s00253-006-0775-x] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 11/17/2006] [Accepted: 11/17/2006] [Indexed: 10/23/2022]
Abstract
Phospholipids are present in all living organisms. They are a major component of all biological membranes, along with glycolipids and cholesterol. Enzymes aimed at modifying phospholipids, namely, phospholipases, are consequently widespread in nature, playing very diverse roles from aggression in snake venom to signal transduction and digestion in humans. In this review, we give a general overview of phospholipases A1, A2, C and D from a sequence and structural perspective and their industrial application. The use of phospholipases in industrial processes has grown hand-in-hand with our ability to clone and express the genes in microbial hosts with commercially attractive amounts. Further, the use in industrial processes is increasing by optimizing the enzymes by protein engineering. Here, we give a perspective on the work done to date to express phospholipases in heterologous hosts and the efforts to optimize them by protein engineering. We will draw attention to the industrial processes where phospholipases play a key role and show how the use of a phospholipase for oil degumming leads to substantial environmental benefits. This illustrates a very general trend: the use of enzymes as an alternative to chemical processes to make products often provides a cleaner solution for the industrial processes. In a world with great demands on non-polluting, energy saving technical solutions--white biotechnology is a strong alternative.
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Affiliation(s)
- L De Maria
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark,
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85
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Ben Ali Y, Carrière F, Abousalham A. High-level constitutive expression in Pichia pastoris and one-step purification of phospholipase D from cowpea (Vigna unguiculata L. Walp). Protein Expr Purif 2007; 51:162-9. [PMID: 16949301 DOI: 10.1016/j.pep.2006.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Revised: 07/09/2006] [Accepted: 07/24/2006] [Indexed: 11/24/2022]
Abstract
Phospholipase D (PLD) is one of the main enzymes involved in signal transduction, vesicle trafficking and membrane metabolism processes. Here we describe the heterologous high-yield expression in the yeast Pichia pastoris, one-step purification and characterization of catalytically active PLDalpha from cowpea (Vigna unguiculata L. Walp). Immunoblotting experiments showed that recombinant PLDalpha is recognized by a polyclonal antibody raised against native soybean PLDalpha. A single calcium-dependent octyl-Sepharose chromatography step was used to obtain a highly purified recombinant PLDalpha, as attested by gel electrophoresis, N-terminal amino acid sequence and mass spectrometry data. From 1L of yeast culture medium, about 8 mg of pure recombinant PLDalpha was obtained and the specific activity measured on phosphatidylcholine was 27 micromol/min/mg. Contrary to what was observed previously with Vigna unguiculata PLDalpha expressed in insect cells, no proteolytic degradation of the N-terminal calcium-dependent C2 lipid binding domain was observed here. This functional recombinant PLDalpha should provide a valuable tool for performing detailed studies on the molecular characterization of enzymes as well as structural studies.
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Affiliation(s)
- Yassine Ben Ali
- Enzymology at Interfaces and Physiology of Lipolysis, UPR 9025-IBSM, CNRS, 31, Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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86
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Khatoon H, Talat S, Younus H. Identification and partial characterization of a highly active and stable phospholipase D from Brassica juncea seeds. Int J Biol Macromol 2007; 40:232-6. [PMID: 16949665 DOI: 10.1016/j.ijbiomac.2006.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 07/26/2006] [Accepted: 07/26/2006] [Indexed: 11/29/2022]
Abstract
Phospholipase D (PLD) activity has been identified in some new plant sources i.e. Brassica juncea (mustard) seeds, Zingibar officinale (ginger) rhizomes and Azadirachta indica (neem) leaves with the aim of identifying PLDs that possess high catalytic activity and stability. PLD from mustard seeds (PLD(ms)) exhibited the highest PLD specific activity, which was highly pH and temperature tolerant. PLD(ms) unlike many plant PLDs exhibited high thermal stability. The activity of PLD(ms) is optimum in the millimolar concentration of calcium ions and is independent of phosphatidylinositol-4,5-bisphosphate (PIP2). An active and stable enzyme like PLD(ms) may be utilized in the lipid industry.
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Affiliation(s)
- Hafeeza Khatoon
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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87
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Uesugi Y, Arima J, Iwabuchi M, Hatanaka T. C-terminal loop of Streptomyces phospholipase D has multiple functional roles. Protein Sci 2006; 16:197-207. [PMID: 17189478 PMCID: PMC2203283 DOI: 10.1110/ps.062537907] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have recently shown that two flexible loops of Streptomyces phospholipase D (PLD) affect the catalytic reaction of the enzyme by a comparative study of chimeric PLDs. Gly188 and Asp191 of PLD from Streptomyces septatus TH-2 (TH-2PLD) were identified as the key amino acid residues involved in the recognition of phospholipids. In the present study, we further investigated the relationship between a C-terminal loop of TH-2PLD and PLD activities to elucidate the reaction mechanism and the recognition of the substrate. By analyzing chimeras and mutants in terms of hydrolytic and transphosphatidylation activities, Ala426 and Lys438 of TH-2PLD were identified as the residues associated with the activities. We found that Gly188 and Asp191 recognized substrate forms, whereas residues Ala426 and Lys438 enhanced transphosphatidylation and hydrolysis activities regardless of the substrate form. By substituting Ala426 and Lys438 with Phe and His, respectively, the mutant showed not only higher activities but also higher thermostability and tolerance against organic solvents. Furthermore, the mutant also improved the selectivity of the transphosphatidylation activity. The residues Ala426 and Lys438 were located in the C-terminal flexible loop of Streptomyces PLD separate from the highly conserved catalytic HxKxxxxD motifs. We demonstrated that this C-terminal loop, which formed the entrance of the active well, has multiple functional roles in Streptomyces PLD.
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Affiliation(s)
- Yoshiko Uesugi
- Research Institute for Biological Sciences-Okayama, 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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88
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Choi SY, Huang P, Jenkins GM, Chan DC, Schiller J, Frohman MA. A common lipid links Mfn-mediated mitochondrial fusion and SNARE-regulated exocytosis. Nat Cell Biol 2006; 8:1255-62. [PMID: 17028579 DOI: 10.1038/ncb1487] [Citation(s) in RCA: 343] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 08/10/2006] [Indexed: 11/09/2022]
Abstract
Fusion of vesicles into target membranes during many types of regulated exocytosis requires both SNARE-complex proteins and fusogenic lipids, such as phosphatidic acid. Mitochondrial fusion is less well understood but distinct, as it is mediated instead by the protein Mitofusin (Mfn). Here, we identify an ancestral member of the phospholipase D (PLD) superfamily of lipid-modifying enzymes that is required for mitochondrial fusion. Mitochondrial PLD (MitoPLD) targets to the external face of mitochondria and promotes trans-mitochondrial membrane adherence in a Mfn-dependent manner by hydrolysing cardiolipin to generate phosphatidic acid. These findings reveal that although mitochondrial fusion and regulated exocytic fusion are mediated by distinct sets of protein machinery, the underlying processes are unexpectedly linked by the generation of a common fusogenic lipid. Moreover, our findings suggest a novel basis for the mitochondrial fragmentation observed during apoptosis.
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Affiliation(s)
- Seok-Yong Choi
- Graduate Program in Molecular and Cellular Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5140, USA
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89
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Simon GM, Cravatt BF. Endocannabinoid Biosynthesis Proceeding through Glycerophospho-N-acyl Ethanolamine and a Role for α/β-Hydrolase 4 in This Pathway. J Biol Chem 2006; 281:26465-72. [PMID: 16818490 DOI: 10.1074/jbc.m604660200] [Citation(s) in RCA: 263] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-Acyl ethanolamines (NAEs) are a large class of signaling lipids implicated in diverse physiological processes, including nociception, cognition, anxiety, appetite, and inflammation. It has been proposed that NAEs are biosynthesized from their corresponding N-acyl phosphatidylethanolamines (NAPEs) in a single enzymatic step catalyzed by a phospholipase D (NAPE-PLD). The recent generation of NAPE-PLD(-/-) mice has revealed that these animals possess lower brain levels of saturated NAEs but essentially unchanged concentrations of polyunsaturated NAEs, including the endogenous cannabinoid anandamide. These findings suggest the existence of additional enzymatic routes for the production of NAEs in vivo. Here, we report evidence for an alternative pathway for NAE biosynthesis that proceeds through the serine hydrolase-catalyzed double-deacylation of NAPE to generate glycerophospho-NAE, followed by the phosphodiesterase-mediated cleavage of this intermediate to liberate NAE. Furthermore, we describe the functional proteomic isolation and identification of a heretofore uncharacterized enzyme alpha/beta-hydrolase 4 (Abh4) as a lysophospholipase/phospholipase B that selectively hydrolyzes NAPEs and lysoNAPEs. Abh4 accepts lysoNAPEs bearing both saturated and polyunsaturated N-acyl chains as substrates and displays a distribution that closely mirrors lysoNAPE-lipase activity in mouse tissues. These results support the existence of an NAPE-PLD-independent route for NAE biosynthesis and suggest that Abh4 plays a role in this metabolic pathway by acting as a (lyso)NAPE-selective lipase.
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Affiliation(s)
- Gabriel M Simon
- Skaggs Institute for Chemical Biology and Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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90
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Han JH, Kerrison N, Chothia C, Teichmann SA. Divergence of interdomain geometry in two-domain proteins. Structure 2006; 14:935-45. [PMID: 16698554 DOI: 10.1016/j.str.2006.01.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 12/23/2005] [Accepted: 01/18/2006] [Indexed: 10/24/2022]
Abstract
For homologous protein chains composed of two domains, we have determined the extent to which they conserve (1) their interdomain geometry and (2) the molecular structure of the domain interface. This work was carried out on 128 unique two-domain architectures. Of the 128, we find 75 conserve their interdomain geometry and the structure of their domain interface; 5 conserve their interdomain geometry but not the structure of their interface; and 48 have variable geometries and divergent interface structure. We describe how different types of interface changes or the absence of an interface is responsible for these differences in geometry. Variable interdomain geometries can be found in homologous structures with high sequence identities (70%).
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Affiliation(s)
- Jung-Hoon Han
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
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91
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Fedeli C, Carrea G, Monti D. On the effects of site-specific mutations on activity and expression of the Streptomyces PMF phospholipase D. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.molcatb.2006.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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92
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Levy BD, Hickey L, Morris AJ, Larvie M, Keledjian R, Petasis NA, Bannenberg G, Serhan CN. Novel polyisoprenyl phosphates block phospholipase D and human neutrophil activation in vitro and murine peritoneal inflammation in vivo. Br J Pharmacol 2006; 146:344-51. [PMID: 16041402 PMCID: PMC1440714 DOI: 10.1038/sj.bjp.0706338] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Leukocyte production of reactive oxygen species (ROS) is an essential component of the antimicrobial armament mounted during host defense, but when released to the extracellular milieu ROS can also injure host tissues and provoke inflammation. Polyisoprenyl phosphates (PIPPs) are constituents of human leukocyte membranes that regulate pivotal intracellular enzymes, such as phospholipase D (PLD). We prepared new PIPP mimetics and studied their impact in vivo on leukocyte activation, including ROS generation, in acute inflammation. In a stereospecific and concentration-dependent manner, the PIPP mimetics directly regulated Streptomyces chromofuscus phospholipase D (sPLD) action. The IC(50) for a (Z)-isomer of endogenous presqualene diphosphate (PSDP) was 100 nM. Structure-activity relationships were also determined for PIPP mimetic inhibition of recombinant human PLD1b, a prominent isoform in human leukocytes. The PIPP mimetic rank order for PLD1b inhibition differed from sPLD, although the (Z)-PSDP isomer remained the most potent PIPP mimetic for inhibition of both enzymes. Truncation of PLD1b to its catalytic core uncovered potential regulatory roles for both PSDP's isoprenoid and diphosphate moieties. The (Z)-PSDP isomer reduced ROS production by activated human leukocytes and decreased murine neutrophil accumulation (65.6%) and ROS production (38.5%) in vivo during zymosan A-initiated peritonitis. When administered intraperitoneally 2 h after zymosan A, the (Z)-PSDP isomer decreased in vivo neutrophil accumulation (72.5%) and ROS generation (74.4%) 6 h later in peritoneal exudates. Together, these results provide new means to protect and control unchecked inflammatory responses that characterize many human diseases.
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Affiliation(s)
- Bruce D Levy
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, U.S.A
- Department of Medicine, Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, U.S.A
| | - Lorraine Hickey
- Department of Medicine, Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, U.S.A
| | - Andrew J Morris
- Department of Cell and Developmental Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Mykol Larvie
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, U.S.A
| | - Raquel Keledjian
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Nicos A Petasis
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Gerard Bannenberg
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, U.S.A
| | - Charles N Serhan
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, U.S.A
- Author for correspondence:
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93
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Lerchner A, Mansfeld J, Schäffner I, Schöps R, Beer HK, Ulbrich-Hofmann R. Two highly homologous phospholipase D isoenzymes from Papaver somniferum L. with different transphosphatidylation potential. Biochim Biophys Acta Mol Cell Biol Lipids 2005; 1737:94-101. [PMID: 16257263 DOI: 10.1016/j.bbalip.2005.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 09/09/2005] [Accepted: 09/21/2005] [Indexed: 11/22/2022]
Abstract
The genes of two phospholipase D (PLD) isoenzymes, PLD1 and PLD2, from poppy seedlings (2829 and 2828 bp) were completely sequenced. The two genes have 96.9% identity in the encoding region and can be assigned to the alpha-type of plant PLDs. The corresponding amino acid sequences do not contain any signal sequences. One Asn-glycosylation site, six and two phosphorylation sites for protein kinase C and tyrosine kinase, respectively, and two phosphatidylinositol-4,5-bisphosphate binding motifs could be identified. Like in most plant PLDs, two HKD motifs and one C2 domain are present. PLD1 and PLD2 have ten and nine cysteine residues. The two enzymes were expressed in E. coli and purified to homogeneity by Ca2+ ion-mediated hydrophobic interaction chromatography. The Ca2+ ion concentration needed for carrier binding of the two enzymes in chromatography as well as for optimum activity was found to be considerably higher (>100 mM) than with other alpha-type plant PLDs. Although PLD1 and PLD2 differ in eleven amino acids only, they showed remarkable differences in their transphosphatidylation activity. Two amino acid exchanges within and near the first HKD motif contribute to this difference as shown by the A349E/E352Q-variant of PLD2.
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Affiliation(s)
- Alexandra Lerchner
- Martin-Luther University Halle-Wittenberg, Department of Biochemistry/Biotechnology, Kurt Mothes Str. 3, D-06120 Halle, Germany
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94
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Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V. Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease. Proc Natl Acad Sci U S A 2005; 102:15797-802. [PMID: 16247004 PMCID: PMC1266039 DOI: 10.1073/pnas.0507949102] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Among all restriction endonucleases known to date, BfiI is unique in cleaving DNA in the absence of metal ions. BfiI represents a different evolutionary lineage of restriction enzymes, as shown by its crystal structure at 1.9-A resolution. The protein consists of two structural domains. The N-terminal catalytic domain is similar to Nuc, an EDTA-resistant nuclease from the phospholipase D superfamily. The C-terminal DNA-binding domain of BfiI exhibits a beta-barrel-like structure very similar to the effector DNA-binding domain of the Mg(2+)-dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors. BfiI presumably evolved through domain fusion of a DNA-recognition element to a nonspecific nuclease akin to Nuc and elaborated a mechanism to limit DNA cleavage to a single double-strand break near the specific recognition sequence. The crystal structure suggests that the interdomain linker may act as an autoinhibitor controlling BfiI catalytic activity in the absence of a specific DNA sequence. A psi-blast search identified a BfiI homologue in a Mesorhizobium sp. BNC1 bacteria strain, a plant symbiont isolated from an EDTA-rich environment.
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Affiliation(s)
- Saulius Grazulis
- Laboratory of Protein-DNA Interaction, Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania.
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95
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Uhm TB, Li T, Bao J, Chung G, Ryu DD. Analysis of phospholipase D gene from Streptoverticillium reticulum and the effect of biochemical properties of substrates on phospholipase D activity. Enzyme Microb Technol 2005. [DOI: 10.1016/j.enzmictec.2005.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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96
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Phospholipases: Occurrence and production in microorganisms, assay for high-throughput screening, and gene discovery from natural and man-made diversity. J AM OIL CHEM SOC 2005. [DOI: 10.1007/s11746-005-1131-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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97
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Zhu Y, Huang W, Lee SSK, Xu W. Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis. EMBO Rep 2005; 6:681-7. [PMID: 15947782 PMCID: PMC1369109 DOI: 10.1038/sj.embor.7400448] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2004] [Revised: 05/04/2005] [Accepted: 05/05/2005] [Indexed: 01/07/2023] Open
Abstract
Polyphosphate (polyP), a linear polymer of hundreds of orthophosphate residues, exists in all tested cells in nature, from pathogenic bacteria to mammals. In bacteria, polyP has a crucial role in stress responses and stationary-phase survival. Polyphosphate kinase (PPK) is the principal enzyme that catalyses the synthesis of polyP in bacteria. It has been shown that PPK is required for bacterial motility, biofilm formation and the production of virulence factors. PPK inhibitors may thus provide a unique therapeutic opportunity against antibiotic-resistant pathogens. Here, we report crystal structures of full-length Escherichia coli PPK and its complex with AMPPNP (beta-gamma-imidoadenosine 5-phosphate). PPK forms an interlocked dimer, with each 80 kDa monomer containing four structural domains. The PPK active site is located in a tunnel, which contains a unique ATP-binding pocket and may accommodate the translocation of synthesized polyP. The PPK structure has laid the foundation for understanding the initiation of polyP synthesis by PPK.
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Affiliation(s)
- Ye Zhu
- Department of Biological Structure, Box 357420, University of Washington, Seattle, Washington 98195, USA
| | - Weijun Huang
- Department of Biological Structure, Box 357420, University of Washington, Seattle, Washington 98195, USA
| | - Sam S K Lee
- ICOS Corporation, Bothell, Washington 98021, USA
| | - Wenqing Xu
- Department of Biological Structure, Box 357420, University of Washington, Seattle, Washington 98195, USA
- Tel: + 1 206 221 5609; Fax: +1 206 543 1524; E-mail:
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98
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Uesugi Y, Mori K, Arima J, Iwabuchi M, Hatanaka T. Recognition of phospholipids in Streptomyces phospholipase D. J Biol Chem 2005; 280:26143-51. [PMID: 15899903 DOI: 10.1074/jbc.m414319200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To investigate the contribution of amino acid residues to the enzyme reaction of Streptomyces phospholipase D (PLD), we constructed a chimeric gene library between two highly homologous plds, which indicated different activity in transphosphatidylation, using RIBS (repeat-length independent and broad spectrum) in vivo DNA shuffling. By comparing the activities of chimeras, six candidate residues related to transphosphatidylation activity were shown. Based on the above result, we constructed several mutants to identify the key residues involved in the recognition of phospholipids. By kinetic analysis, we identified that Gly188 and Asp191 of PLD from Streptomyces septatus TH-2, which are not present in the highly conserved catalytic HXKXXXXD (HKD) motifs, are key amino acid residues related to the transphosphatidylation activity. To investigate the role of two residues in the recognition of phospholipids, the effects of these residues on binding to substrates were analyzed by surface plasmon spectroscopy. The result suggests that Gly188 and Asp191 are involved in the recognition of phospholipids in correlation with the N-terminal HKD motif. Furthermore, this study also provides experimental evidence that the N-terminal HKD motif contains the catalytic nucleophile, which attacks the phosphatidyl group of the substrate.
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Affiliation(s)
- Yoshiko Uesugi
- Research Institute for Biological Sciences, Okayama, 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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99
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Negishi T, Mukaihara T, Mori K, Nishikido H, Kawasaki Y, Aoki H, Kodama M, Uedaira H, Uesugi Y, Iwabuchi M, Hatanaka T. Identification of a key amino acid residue of Streptomyces phospholipase D for thermostability by in vivo DNA shuffling. Biochim Biophys Acta Gen Subj 2005; 1722:331-42. [PMID: 15777623 DOI: 10.1016/j.bbagen.2005.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2004] [Revised: 12/20/2004] [Accepted: 01/04/2005] [Indexed: 11/20/2022]
Abstract
To isolate thermostability-related amino acid residues of Streptomyces phospholipase D (PLD), we constructed a chimeral genes library between two highly homologous plds, which exhibited different thermostabilities, by an in vivo DNA shuffling method using Escherichia coli that has a mutation of a single-stranded DNA-binding protein gene. To confirm the location of the recombination site, we carried out the restriction mapping of 68 chimeral pld genes. The recombination sites were widely dispersed over the entire pld sequence. Moreover, we examined six chimeral PLDs by comparing their thermostabilities with those of parental PLDs. To identify a thermostability-related amino acid residue, we investigated the thermostability of chimera C that was the most thermolabile among the six chimeras. We identified the thermostability-related factor Gly-188, which is located in the alpha-7 helix of PLD from Streptomyces septatus TH-2 (TH-2PLD). TH-2PLD mutants, in which Gly-188 was substituted with Phe, Val or Trp, exhibited higher thermostabilities than that of the parental PLD. Gly-188 substituted with the Phe mutant, which was the most stable among the mutants, showed an enzyme activity almost the same as that of TH-2PLD as determine by kinetic analysis.
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Affiliation(s)
- Tomofumi Negishi
- Research Institute for Biological Sciences, Okayama (RIBS), 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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100
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Ulbrich-Hofmann R, Lerchner A, Oblozinsky M, Bezakova L. Phospholipase D and its application in biocatalysis. Biotechnol Lett 2005; 27:535-44. [PMID: 15973486 DOI: 10.1007/s10529-005-3251-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 02/24/2005] [Indexed: 10/25/2022]
Abstract
Phospholipase D (PLD) from plants or microorganisms is used as biocatalyst in the transformation of phospholipids and phospholipid analogs in both laboratory and industrial scale. In recent years the elucidation of the primary structure of many PLDs from several sources, as well as the resolution of the first crystal structure of a microbial PLD, have yielded new insights into the structural basis and the catalytic mechanism of this catalyst. This review summarizes some new results of PLD research in the light of application.
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Affiliation(s)
- Renate Ulbrich-Hofmann
- Department of Biochemistry/Biotechnology, Martin-Luther University Halle-Wittenberg, D-06120, Halle, Germany.
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