Membrane anchoring and ionentry dynamics in ptype atpase. Each of the following phrases describes abc transporters, p type atpases, or both. Preferential delivery of zinc to developing tissues in. Surprisingly, among the multiple members of ptype atpases known so far 11,16,19,21,the promoters for only a few ptype atpase genes have been identified. Ptype atpases are transmembrane proteins that play a crucial role in the transport of a wide variety of cations across membranes and they are vital for ion homeostasis and heavy metal detoxification. There are many different classes of patpases, which transports a specific type of ion. The structure of type ib ptype atpase copa is now solved in its e2p state. Interdomain motions of the ndomain of the kdpfabc complex, a p type atpase, are not driven by atpinduced conformational changes. Each of the following phrases describes abc transporters, ptype atpases, or both. The identity of cod1p as a p type atpase and its importance in the normal functioning of the er suggests that it functions to control the balance of one or more ions in the lumen of the er. Atp8b1 is a type4 ptype atpase that maintains lipid balance by translocating phospholipids, such as phosphatidylserine, from the outer to the inner leaflets of membrane bilayers. Bioinformatic characterization of ptype atpases encoded within.
F type pumps are named from the original fof 1 nomenclature of the mitochondrial atp synthase. Our analysis identified 43 members of the ptype atpase family in rice fig. P type atpase was named based on the presence of an intermediate phosphorylated process occurring during catalyzing, and first described as a pump that was thought to be associated with the transport of sodium ions in 1957. Atp8b1 also transports cardiolipin, a mitochondrial membrane phospholipid ray et al.
Our analysis identified 43 members of the p type atpase family in rice fig. Inventory of the superfamily of ptype ion pumps in arabidopsis. Here, we address the central question of how the transported cu. Of these helices, m1m6 are conserved among members of the p atpase family. Abc transporters and p type atpase transporters are membrane pumps that move ions and molecules across membranes. We and others have recently identified another ptype atpase in yeast, cod1pspf1p, that adds a new dimension to the regulation of er ion supply suzuki and shimma, 1999. Coppertransporting ptype atpases use a unique ionrelease. The cdna encodes a protein of 1,098 aa and was designated pca1 ptype ca 2. The p type atpase database was launched as part of a project performed at the traplabs, department of plant biology, the faculty of life sciences of the copenhagen university, copenhagen, denmark. Here, we identified 419 ptype atpase genes from seven rosaceae species pyrus bretschneideri, malus domestica. The close pairing of similar isoforms in rice and arabidopsis suggests potential orthologous relationships for all 43. The structure and mechanism of vtype atpases differs from the ptype active transporters.
Ijms free fulltext hvpaa1 encodes a ptype atpase, a. We present an approach to ptype atpase sequence classification. We demonstrate here that different point mutations in a ptype atpase could play an important role in resistance, not only to miltefosine, but also to amphotericin b. Three of these transporters, hma2, hma3, and hma4, are closely related to each other and are most similar in sequence to the divalent heavy metal cation transporters of prokaryotes. A ptype atpase required for rice blast disease and.
P 2b contained the most pty pe atpase genes 141 of 419, followed by p 3a 80 of 419, p 1b 75 of 419 and p4 72 of 419, whereas the p 2a 41 of 419 and p5 10 of 419 subfamilies had the fewest members of the seven species fig. Bioinformatic characterization of ptype atpases encoded within the fully sequenced genomes of 26 eukaryotes. The fulllength cdna was isolated from a cdna library and subsequent amplification of the 5. In particular, md simulations have proved valuable in generating and confirming hypotheses relating to the structure and function of ptype atpases. Fatpase, also known as ftype atpase, is an atp synthase found in bacterial plasma membranes, in mitochondrial inner membranes in oxidative phosphorylation, where it is known as complex v, and in chloroplast thylakoid membranes. Abc transporters and ptype atpase transporters are membrane pumps that move ions and molecules across membranes. Function of patpase is to transport a variety of different compounds, like ions and phospholipids, across a membrane using atp hydrolysis for energy. Given the predicted multifunctionality of this protein. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. The yeast proteome database ypd and caenorhabditis elegans proteome.
Here, we explain how to use the information in freely available databases together with computational methods for classification and motif detection to assess whether a protein sequence corresponds to a ptype atpase and if so, which subtype or not. In the following, we describe a detailed practical procedure on how to set up and run a md simulation of a ptype atpase embedded in a lipid bilayer using software free of use for academics. Ptype atpases form a large superfamily of cation and lipid pumps. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
Promoter paper isolation, sequencing, and functional. The v 0 motor, responsible for ion translocation, has six subunits ae. Arabidopsis thaliana has eight genes encoding members of the type 1b heavy metaltransporting subfamily of the ptype atpases. Characteristics of the family are the transient phosphorylation of the transporters at an aspartate residue and the interconversion between e1 and e2 conformations in the activity cycle of the transporters, taken to represent halfchannels facing the cytoplasm and. P 4atpases form heteromeric complexes with cdc50like proteins, and it has been suggested that these act as. Ptype atpase in several rosaceae species including the pear have been identified zhang et al. Origin and evolution of metal ptype atpases in plantae. Atpase involved in the acidification of the stomach in mammals, see hydrogen potassium atpase. Comparative analysis of the ptype atpase gene family in.
Interpro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. The two consensus motifs of p type atpase, dktgtlt motif and gdgxndx motif, are conserved in gmhma1a. The idea that this ion might be calcium first arose from our previous observations of cod1 suppression by manipulating exogenous calcium cronin et al. Genomic comparison of ptype atpase ion pumps in arabidopsis. Ptype atpases transporters iupharbps guide to pharmacology. This response is incorrect, can someone help me ca. Purification and characterization of p type atpases. Fulllength, established ptype atpase sequences were retrieved from the. Subsequently, growth was tested in the presence of various concentrations of different metals and compared to growth of vector. In plants, there are primarily three kinds of proton pumps, the v type atpase, p type atpase and f type atpase. Tissue specific expression of atpases have been well characterized 14,21. P atpases may be composed of one or two polypeptides, and can usually take two main conformations, e1 and e2. A mutation database for this pump is maintained by jens peter andersen. Tcdb superfamilies transporter classification database.
Ptype atpases are integral membrane transporters that play important roles in transmembrane transport in plants. Haupt m, bramkamp m, coles m, altendorf k, kessler h. Four major domains are ubiquitously present in ptype atpases. Bioinformatic characterization of p type atpases encoded within the fully sequenced genomes of 26 eukaryotes. To be specific, the protein is a part of the p type atpase family. Here, we report that rice oryza sativa heavy metal atpase2 oshma2, a member of ptype atpases, is involved in preferential delivery of zinc to the developing tissues. The p type atpase database is supported by the swiss institute of bioinformatics and the traplabs. Here we show crystal structures at a resolution of 2. Developing tissues such as meristems and reproductive organs require high zinc, but the molecular mechanisms of how zinc taken up by the roots is preferentially delivered to these tissues with low transpiration are unknown. Ftype pumps are named from the original fof 1 nomenclature of the mitochondrial atp synthase. Ipr023298 ptype atpase, transmembrane domain superfamily. The ptype atpase database is supported by the swiss institute of bioinformatics and the traplabs.
Different mutations in a ptype atpase transporter in. Complete sequences can be found at the ptype atpase database web site. The gdgxndx motif is involved in atp binding williams et al. Furthermore, macrophageinfecting amastigotes that are resistant to one drug are crossresistant. Interdomain motions of the ndomain of the kdpfabc complex, a ptype atpase, are not driven by atpinduced conformational changes. P type atpases adopt different conformations during their transport cycle, including autophosphorylated forms. Pde1 encodes a ptype atpase involved in appressoriummediate plant infection by the rice blast fungus magnaporthe grisea. Characteristics of the family are the transient phosphorylation of the transporters at an aspartate residue and the interconversion between e1 and e2 conformations in the activity cycle of the transporters.
Members of the ptype atpase ion pump superfamily are found in all three. To ensure that all possible p type atpase genes were identified, multiple independent sequences were searched in several different ways. P 1batpase constitutes one of the five major subfamilies of ptype atpases. To ensure that all possible ptype atpase genes were identified, multiple independent sequences were searched in several different ways. It uses a proton gradient to drive atp synthesis by allowing the passive flux of protons across the membrane down their electrochemical gradient and using the energy. The rcsb pdb also provides a variety of tools and resources. Patpases may be composed of one or two polypeptides, and can usually take two main conformations, e1 and e2. Evolution of substrate specificities in the ptype atpase. The vtype atpase is most prominently associated with lysosomes in mammals, but also appears to be expressed on the plasma membrane and neuronal synaptic vesicles. The ptype atpase database was launched as part of a project performed at the traplabs, department of plant biology, the faculty of life sciences of the copenhagen university, copenhagen, denmark.
Both arabidopsis and rice have representative members in all five major subfamilies of ptype atpases. Structural biochemistrymembrane proteinsptype atpases. All ptype atpase proteins share a common structural core of intracellular a actuator, p phosphorylation. Eukarya arabidopsis thaliana caenorhabditis elegans drosophila melanogaster homo sapiens saccharomyces cerevisiae. Cod1pspf1p is a ptype atpase involved in er function and. Here, we explain how to use the information in freely available databases together with computational methods for classification and motif detection to assess whether a protein sequence corresponds to a p type atpase and if so, which subtype or not. Ptype atpase heavy metal transporters with roles in. There is a general stay at home order until the end of may, which northwestern university is also following. Structurally, all ptype atpases share certain common points. Ipr004014 cationtransporting ptype atpase, nterminal. As a member of the wwpdb, the rcsb pdb curates and annotates pdb data according to agreed upon standards.
To determine the function of these transporters in metal. Md simulations of ptype atpases in a lipid bilayer system. Intracellular targeting signals and lipid specificity. Class ib p type atpases p ib type atpases perform active transport of heavy metals across cellular membranes and are of crucial importance for heavy metal homeostasis. The v 1 motor, responsible for atp turnover, has eight subunits with a composition of ah. An unusual and vital protein with guanylate cyclase and p4. Note that membrane pumps containing atpbinding cassette domains are referred to as abc transporters.
Cod1p belongs to the type v subfamily of ptype atpases that are broadly conserved in eukaryotes but for which no ionic substrates have yet been identified axelsen and palmgren, 1998. In arabidopsis thaliana, eight metal ptype atpases have been. These all form phosphorylated intermediates in the pump mechanism, like that shown for the na,k atpase in figure 2. Mouse genome database mgd, gene expression database gxd, mouse models of human cancer database mmhcdb formerly mouse tumor biology mtb, gene ontology go. Vtype atpase transporters iupharbps guide to pharmacology. The structure of type ib p type atpase copa is now solved in its e2p state. Atp8b1 is a type 4 p type atpase that maintains lipid balance by translocating phospholipids, such as phosphatidylserine, from the outer to the inner leaflets of membrane bilayers. We demonstrate here that different point mutations in a p type atpase could play an important role in resistance, not only to miltefosine, but also to amphotericin b. The ptype atpase database was launched as part of a project performed at the traplabs, department of plant biology, the faculty of life sciences of the copenhagen university, copenhagen, denmark the ptype atpase database is supported by the swiss institute of bioinformatics and the traplabs. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists. In contrast, helices m7m10 mainly function as a membrane anchor to provide stability to the mdomain norimatsu et al. Welcome to dictybase, your central resource for dictyostelid genomics news april 30, 2020 dicty stock center.
Ptype atpases are atp fuelled ion pumps with a single catalytic subunit, and. Our genome searches identified a single putative gc in the parasite database toxodb gajria et al, 2008, comprising multiple ptype atpase motifs at its n terminus and two nucleotide cyclase domains termed as gc1 and gc2 based on the evidence herein at the c terminus. Thus, it is likely that a more widely conserved ptype atpase is responsible for er ion. Author summary miltefosine and amphotericin b are two leading molecules in the fight against the vectorborne disease leishmaniasis. The initial screen of the embl and swissprot databases was performed with the prosite consensus sequence for p type atpases dktgt,sl,i,v,mt,i. This enzyme belongs to the family of hydrolases, specifically those acting on acid anhydrides to catalyse transmembrane movement of substances. Members of the p 4 subfamily of ptype atpases are believed to catalyze flipping of phospholipids across cellular membranes, in this way contributing to vesicle biogenesis in the secretory and endocytic pathways. Three of these transporters, hma2, hma3, and hma4, are closely related to each other and are most similar in sequence to. The ptype atpases, also known as e 1e 2 atpases, are a large group of evolutionarily related ion and lipid pumps that are found in bacteria, archaea, and eukaryotes. Ipr005775 ptype atpase subfamily iic, subunit alpha.
B the centerofmass com for the mdomain and mb helix, respectively, for the three. As of june 2007, 400 unique and confirmed members of the ptype atpase family have been discovered. As of june 2007, 400 unique and confirmed members of the p type atpase family have been discovered. Ptype atpases adopt different conformations during their transport cycle, including autophosphorylated forms. These enzymes have a significant impact on cellular funciton. The m domain consists of the 610 transmembrane helices and the small intertransmembrane loops that connect them. Based on the classification of subfamilies in arabidopsis, all the ptype atpase genes in rosaceae species could be divided into five major subfamilies. Multiple alignments between all of the p 1b atpase sequences indicate that hma1, hma2. The ptype atpases, also known as e1e2 atpases, are a large group of evolutionarily related ion and lipid pumps that are found in bacteria, archaea, and eukaryotes.
Plant p 1b atpases have been classified that are expected to be involved in the transport of heavy metals. Computational classification of ptype atpases springerlink. Evolution of ptype atpases connecting repositories. There are many different classes of patpases, which transport specific types of. A toolbox for classification and analysis of ptype atpases. The v type atpase is most prominently associated with lysosomes in mammals, but also appears to be expressed on the plasma membrane and neuronal synaptic vesicles. We combine protein signatures from a number of member databases into a. Arabidopsis thaliana has eight genes encoding members of the type 1 b heavy metaltransporting subfamily of the ptype atpases. The position of this sequence in the phylogenetic tree might change. Function of p atpase is to transport a variety of different compounds, like ions and phospholipids, across a membrane using atp hydrolysis for energy. However, a comprehensive analysis of the ptype atpase gene family has not been conducted in chinese white pear pyrus bretschneideri or other rosaceae species. The initial screen of the embl and swissprot databases was performed with the prosite consensus sequence for ptype atpases dktgt,sl,i,v,mt,i. A ptype atpase required for rice blast disease and induction.
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