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Scott BM, Koh K, Rix GD. Structural and functional profile of phytases across the domains of life. Curr Res Struct Biol 2024; 7:100139. [PMID: 38562944 PMCID: PMC10982552 DOI: 10.1016/j.crstbi.2024.100139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Phytase enzymes are a crucial component of the natural phosphorus cycle, as they help make phosphate bioavailable by releasing it from phytate, the primary reservoir of organic phosphorus in grain and soil. Phytases also comprise a significant segment of the agricultural enzyme market, used primarily as an animal feed additive. At least four structurally and mechanistically distinct classes of phytases have evolved in bacteria and eukaryotes, and the natural diversity of each class is explored here using advances in protein structure prediction and functional annotation. This graphical review aims to provide a succinct description of the major classes of phytase enzymes across phyla, including their structures, conserved motifs, and mechanisms of action.
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Affiliation(s)
- Benjamin M. Scott
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, S7N 4L8, Saskatoon, Saskatchewan, Canada
| | - Kevin Koh
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, S7N 4L8, Saskatoon, Saskatchewan, Canada
| | - Gregory D. Rix
- Inspiralis Ltd., Innovation Centre, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK
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2
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Burroughs A, Aravind L. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. NAR Genom Bioinform 2023; 5:lqad029. [PMID: 36968430 PMCID: PMC10034599 DOI: 10.1093/nargab/lqad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The protein-tyrosine/dual-specificity phosphatases and rhodanese domains constitute a sprawling superfamily of Rossmannoid domains that use a conserved active site with a cysteine to catalyze a range of phosphate-transfer, thiotransfer, selenotransfer and redox activities. While these enzymes have been extensively studied in the context of protein/lipid head group dephosphorylation and various thiotransfer reactions, their overall diversity and catalytic potential remain poorly understood. Using comparative genomics and sequence/structure analysis, we comprehensively investigate and develop a natural classification for this superfamily. As a result, we identified several novel clades, both those which retain the catalytic cysteine and those where a distinct active site has emerged in the same location (e.g. diphthine synthase-like methylases and RNA 2' OH ribosyl phosphate transferases). We also present evidence that the superfamily has a wider range of catalytic capabilities than previously known, including a set of parallel activities operating on various sugar/sugar alcohol groups in the context of NAD+-derivatives and RNA termini, and potential phosphate transfer activities involving sugars and nucleotides. We show that such activities are particularly expanded in the RapZ-C-DUF488-DUF4326 clade, defined here for the first time. Some enzymes from this clade are predicted to catalyze novel DNA-end processing activities as part of nucleic-acid-modifying systems that are likely to function in biological conflicts between viruses and their hosts.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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3
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Zhao T, Yong X, Zhao Z, Dolce V, Li Y, Curcio R. Research status of Bacillus phytase. 3 Biotech 2021; 11:415. [PMID: 34485008 DOI: 10.1007/s13205-021-02964-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022] Open
Abstract
Phytic acid is abundant in seeds, roots and stems of plants, it acts as an anti-nutrient in food and feed industry, since it affects the absorption of nutrients by humans and monogastric animals. Furthermore, phosphorus produced through its decomposition by microorganisms can cause environmental pollution. Phytase degrades phytic acid generating precursors of inositol that can be used in clinical practice; in addition, phytase treatment can minimize the anti-nutritional effect of phytic acid. The use of phytase synthesized from Bacillus is more advantageous due to its high activity. Additionally, its good heat resistance under neutral conditions greatly fills the gap of commercial utilization of acid phytase. In this review, we summarize the latest research results on Bacillus phytase, including its physiological and biochemical characteristics, molecular structure information, calcium effects on its catalytic activity and stability, its catalytic mechanism and molecular modification.
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Affiliation(s)
- Ting Zhao
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Xihao Yong
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- Faculty of Bioengineering, Sichuan University of Science and Engineering, Zigong, People's Republic of China
| | - Ziming Zhao
- Faculty of Bioengineering, Sichuan University of Science and Engineering, Zigong, People's Republic of China
| | - Vincenza Dolce
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Yuan Li
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Rosita Curcio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
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4
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Le HTT, Cho Y, Lee S, Kim Y, Kim K, Park SG, Park BC, Cho S. PTP Inhibitor XIX Inhibits DUSP22 by Conformational Change. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hien Thi Thu Le
- College of PharmacyChung‐Ang University Seoul 06974 Republic of Korea
| | - Young‐Chang Cho
- College of PharmacyChonnam National University Gwangju 61186 Republic of Korea
| | - Sewoong Lee
- College of PharmacyChung‐Ang University Seoul 06974 Republic of Korea
| | - Yang‐Gyun Kim
- Department of ChemistrySungkyunkwan University Suwon 16419 Republic of Korea
| | - Kwonseop Kim
- College of PharmacyChonnam National University Gwangju 61186 Republic of Korea
| | - Sung Goo Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
| | - Byoung Chul Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
| | - Sayeon Cho
- College of PharmacyChung‐Ang University Seoul 06974 Republic of Korea
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5
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Characteristics of the First Protein Tyrosine Phosphatase with Phytase Activity from a Soil Metagenome. Genes (Basel) 2019; 10:genes10020101. [PMID: 30700057 PMCID: PMC6409689 DOI: 10.3390/genes10020101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/19/2019] [Accepted: 01/24/2019] [Indexed: 11/30/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) fulfil multiple key regulatory functions. Within the group of PTPs, the atypical lipid phosphatases (ALPs) are known for their role as virulence factors associated with human pathogens. Another group of PTPs, which is capable of using inositol-hexakisphosphate (InsP6) as substrate, are known as phytases. Phytases play major roles in the environmental phosphorus cycle, biotechnology, and pathogenesis. So far, all functionally characterized PTPs, including ALPs and PTP-phytases, have been derived exclusively from isolated microorganisms. In this study, screening of a soil-derived metagenomic library resulted in identification of a gene (pho16B), encoding a PTP, which shares structural characteristics with the ALPs. In addition, the characterization of the gene product (Pho16B) revealed the capability of the protein to use InsP6 as substrate, and the potential of soil as a source of phytases with so far unknown characteristics. Thus, Pho16B represents the first functional environmentally derived PTP-phytase. The enzyme has a molecular mass of 38 kDa. The enzyme is promiscuous, showing highest activity and affinity toward naphthyl phosphate (Km 0.966 mM). Pho16B contains the HCXXGKDR[TA]G submotif of PTP-ALPs, and it is structurally related to PtpB of Mycobacterium tuberculosis. This study demonstrates the presence and functionality of an environmental gene codifying a PTP-phytase homologous to enzymes closely associated to bacterial pathogenicity.
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Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases. mBio 2019; 10:mBio.01966-18. [PMID: 30696742 PMCID: PMC6355987 DOI: 10.1128/mbio.01966-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphatases, including phytases, play a major role in cell metabolism, phosphorus cycle, biotechnology, and pathogenic processes. Nevertheless, their discovery by functional metagenomics is challenging. Here, soil metagenomic libraries were successfully screened for genes encoding phosphatase activity. In this context, we report the largest number and diversity of phosphatase genes derived from functional metagenome analysis. Two of the detected gene products carry domains which have never been associated with phosphatase activity before. One of these domains, the SNARE-associated domain DedA, harbors a so-far-overlooked motif present in numerous bacterial SNARE-associated proteins. Our analysis revealed a previously unreported phytase activity of the alkaline phosphatase and sulfatase superfamily (cl23718) and of purple acid phosphatases from nonvegetal origin. This suggests that the classical concept comprising four classes of phytases should be modified and indicates high performance of our screening method for retrieving novel types of phosphatases/phytases hidden in metagenomes of complex environments.IMPORTANCE Phosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth's phosphatase pools.
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Gessler NN, Serdyuk EG, Isakova EP, Deryabina YI. Phytases and the Prospects for Their Application (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818040087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Angelovičová M, Mellen M, Zajác P, Čapla J, Angelovič M. Tibia mineralization of chickens determined to meat production using a microbial phytase. POTRAVINARSTVO 2018. [DOI: 10.5219/805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The target of the research was 6-phytase of microbial origin. It was used in feed mixtures for chickens determined to meat production. Its effect has been studied in relation to the tibia mineralization by calcium, phosphorus and magnesium. 6-phytase is a product of Aspergillus oryzae. That was obtained by means of biotechnological processes of production of commercially available enzymes. It was incorporated in the feed mixtures 0.1%. In a 38-day feeding trial, 300 one-day-old, as hatched, Cobb 500 chickens determined to meat production (100 birds per group) were fed on one concentrations of dietary non-phytate phosphorus (2.32, 2.31 g.kg-1, respectively and supplemental microbial phytase (0 and 500 FTU.kg-1 feed mixtures). Control group was used to compare the results and control feed mixtures contained 4.5 g.kg-1 without microbial phytase. At days 40 it was selected 6 birds in every group, which were slaughter in accordance with the principles of welfare. Left tibias of every bird were used to determination of calcium, phosphorus and magnesium contents. According to in vivo, it was found that the addition of microbial phytase to reduced dietary non-phytate phosphorus increased concentrations of calcium (Ca), phosphorus (P) and magnesium (Mg) in tibia. The differences among groups were statistically significant (p <0.05). It was concluded that reducing of dietary non-phytate phosphorus on the 2.32, 2.31 g.kg-1, respectively, by monocalcium phosphate and microbial phytase supplementation in feed mixtures facilitated tibia mineralization at chicken determined to meat production.
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Sharma R, Kumar P, Kaushal V, Das R, Kumar Navani N. A novel protein tyrosine phosphatase like phytase from Lactobacillus fermentum NKN51: Cloning, characterization and application in mineral release for food technology applications. BIORESOURCE TECHNOLOGY 2018; 249:1000-1008. [PMID: 29145111 DOI: 10.1016/j.biortech.2017.10.106] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
A novel protein tyrosine phosphatase like phytase (PTPLP), designated as PhyLf from probiotic bacterium Lactobacillus fermentum NKN51 was identified, cloned, expressed and characterized. The recombinant PhyLf showed specific activity of 174.5 U/mg. PhyLf exhibited strict specificity towards phytate and optimum temperature at 60 °C, pH 5.0 and ionic strength of 100 mM. Km and Kcat of PhyLf for phytate were 0.773 mM and 84.31 s-1, respectively. PhyLf exhibited high resistance against oxidative inactivation. PhyLf shares no homology, sans the active site with reported PTLPs, warranting classification as a new subclass. Dephytinization of durum wheat and finger millet under in vitro gastrointestinal conditions using PhyLf enhanced the bioaccessibility of mineral ions. Probiotic origin, phytate specificity, resistance to oxidative environment and gastric milieu coupled with ability to release micronutrients are unique properties of PhyLf which present a strong case for its use in ameliorating nutritional value of cereals and animal feed.
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Affiliation(s)
- Rekha Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Piyush Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Vandana Kaushal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Rahul Das
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata 741246, India
| | - Naveen Kumar Navani
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
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10
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Abstract
In higher eukaryotes, the Tyr phosphorylation status of cellular proteins results from the coordinated action of Protein Tyrosine Kinases (PTKs) and Protein Tyrosine Phosphatases (PTPs). PTPs have emerged as highly regulated enzymes with diverse substrate specificity, and proteins with Tyr-dephosphorylation or Tyr-dephosphorylation-like properties can be clustered as the PTPome. This includes proteins from the PTP superfamily, which display a Cys-based catalytic mechanism, as well as enzymes from other gene families (Asp-based phosphatases, His-based phosphatases) that have converged in protein Tyr-dephosphorylation-related functions by using non-Cys-based catalytic mechanisms. Within the Cys-based members of the PTPome, classical PTPs dephosphorylate specific phosphoTyr (pTyr) residues from protein substrates, whereas VH1-like dual-specificity PTPs dephosphorylate pTyr, pSer, and pThr residues, as well as nonproteinaceous substrates, including phosphoinositides and phosphorylated carbohydrates. In addition, several PTPs have impaired catalytic activity as a result of amino acid substitutions at their active sites, but retain regulatory functions related with pTyr signaling. As a result of their relevant biological activity, many PTPs are linked to human disease, including cancer, neurodevelopmental, and metabolic diseases, making these proteins important drug targets and molecular markers in the clinic. Here, a brief overview on the biochemistry and physiology of the different groups of proteins that belong to the mammalian PTPome is presented.
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11
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Blüher D, Laha D, Thieme S, Hofer A, Eschen-Lippold L, Masch A, Balcke G, Pavlovic I, Nagel O, Schonsky A, Hinkelmann R, Wörner J, Parvin N, Greiner R, Weber S, Tissier A, Schutkowski M, Lee J, Jessen H, Schaaf G, Bonas U. A 1-phytase type III effector interferes with plant hormone signaling. Nat Commun 2017; 8:2159. [PMID: 29255246 PMCID: PMC5735085 DOI: 10.1038/s41467-017-02195-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 11/13/2017] [Indexed: 11/16/2022] Open
Abstract
Most Gram-negative phytopathogenic bacteria inject type III effector (T3E) proteins into plant cells to manipulate signaling pathways to the pathogen's benefit. In resistant plants, specialized immune receptors recognize single T3Es or their biochemical activities, thus halting pathogen ingress. However, molecular function and mode of recognition for most T3Es remains elusive. Here, we show that the Xanthomonas T3E XopH possesses phytase activity, i.e., dephosphorylates phytate (myo-inositol-hexakisphosphate, InsP6), the major phosphate storage compound in plants, which is also involved in pathogen defense. A combination of biochemical approaches, including a new NMR-based method to discriminate inositol polyphosphate enantiomers, identifies XopH as a naturally occurring 1-phytase that dephosphorylates InsP6 at C1. Infection of Nicotiana benthamiana and pepper by Xanthomonas results in a XopH-dependent conversion of InsP6 to InsP5. 1-phytase activity is required for XopH-mediated immunity of plants carrying the Bs7 resistance gene, and for induction of jasmonate- and ethylene-responsive genes in N. benthamiana.
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Affiliation(s)
- Doreen Blüher
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Debabrata Laha
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Sabine Thieme
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Alexandre Hofer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lennart Eschen-Lippold
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Antonia Masch
- Institute for Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle (Saale), Germany
| | - Gerd Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Igor Pavlovic
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Oliver Nagel
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Antje Schonsky
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Rahel Hinkelmann
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Jakob Wörner
- Institute of Physical Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Nargis Parvin
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Ralf Greiner
- Department of Food Technology and Bioprocess Engineering, Max-Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Mike Schutkowski
- Institute for Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle (Saale), Germany
| | - Justin Lee
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Henning Jessen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.
| | - Gabriel Schaaf
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany.
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany.
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany.
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12
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Bruder LM, Gruninger RJ, Cleland CP, Mosimann SC. Bacterial PhyA protein-tyrosine phosphatase-like myo-inositol phosphatases in complex with the Ins(1,3,4,5)P 4 and Ins(1,4,5)P 3 second messengers. J Biol Chem 2017; 292:17302-17311. [PMID: 28848052 DOI: 10.1074/jbc.m117.787853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/24/2017] [Indexed: 11/06/2022] Open
Abstract
myo-Inositol phosphates (IPs) are important bioactive molecules that have multiple activities within eukaryotic cells, including well-known roles as second messengers and cofactors that help regulate diverse biochemical processes such as transcription and hormone receptor activity. Despite the typical absence of IPs in prokaryotes, many of these organisms express IPases (or phytases) that dephosphorylate IPs. Functionally, these enzymes participate in phosphate-scavenging pathways and in plant pathogenesis. Here, we determined the X-ray crystallographic structures of two catalytically inactive mutants of protein-tyrosine phosphatase-like myo-inositol phosphatases (PTPLPs) from the non-pathogenic bacteria Selenomonas ruminantium (PhyAsr) and Mitsuokella multacida (PhyAmm) in complex with the known eukaryotic second messengers Ins(1,3,4,5)P4 and Ins(1,4,5)P3 Both enzymes bound these less-phosphorylated IPs in a catalytically competent manner, suggesting that IP hydrolysis has a role in plant pathogenesis. The less-phosphorylated IP binding differed in both the myo-inositol ring position and orientation when compared with a previously determined complex structure in the presence of myo-inositol-1,2,3,4,5,6-hexakisphosphate (InsP6 or phytate). Further, we have demonstrated that PhyAsr and PhyAmm have different specificities for Ins(1,2,4,5,6)P5, have identified structural features that account for this difference, and have shown that the absence of these features results in a broad specificity toward Ins(1,2,4,5,6)P5 These features are main-chain conformational differences in loops adjacent to the active site that include the extended loop prior to the penultimate helix, the extended Ω-loop, and a β-hairpin turn of the Phy-specific domain.
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Affiliation(s)
- Lisza M Bruder
- From the Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada and
| | - Robert J Gruninger
- the Lethbridge Research Centre, Agriculture and Agri-Foods Canada, Lethbridge AB T1J 4B1, Canada
| | - Colyn P Cleland
- From the Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada and
| | - Steven C Mosimann
- From the Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada and
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13
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Engineering the residual side chains of HAP phytases to improve their pepsin resistance and catalytic efficiency. Sci Rep 2017; 7:42133. [PMID: 28186144 PMCID: PMC5301473 DOI: 10.1038/srep42133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/06/2017] [Indexed: 11/08/2022] Open
Abstract
Strong resistance to proteolytic attack is important for feed enzymes. Here, we selected three predicted pepsin cleavage sites, L99, L162, and E230 (numbering from the initiator M of premature proteins), in pepsin-sensitive HAP phytases YkAPPA from Yersinia kristensenii and YeAPPA from Y. enterocolitica, which corresponded to L99, V162, and D230 in pepsin-resistant YrAPPA from Y. rohdei. We constructed mutants with different side chain structures at these sites using site-directed mutagenesis and produced all enzymes in Escherichia coli for catalytic and biochemical characterization. The substitutions E230G/A/P/R/S/T/D, L162G/A/V, L99A, L99A/L162G, and L99A/L162G/E230G improved the pepsin resistance. Moreover, E230G/A and L162G/V conferred enhanced pepsin resistance on YkAPPA and YeAPPA, increased their catalytic efficiency 1.3–2.4-fold, improved their stability at 60 °C and pH 1.0–2.0 and alleviated inhibition by metal ions. In addition, E230G increased the ability of YkAPPA and YeAPPA to hydrolyze phytate from corn meal at a high pepsin concentration and low pH, which indicated that optimization of the pepsin cleavage site side chains may enhance the pepsin resistance, improve the stability at acidic pH, and increase the catalytic activity. This study proposes an efficient approach to improve enzyme performance in monogastric animals fed feed with a high phytate content.
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14
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Balaban NP, Suleimanova AD, Valeeva LR, Shakirov EV, Sharipova MR. Structural Characteristics and Catalytic Mechanism of Bacillus β-Propeller Phytases. BIOCHEMISTRY (MOSCOW) 2017; 81:785-93. [PMID: 27677548 DOI: 10.1134/s0006297916080010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
β-Propeller phytases of Bacillus are unique highly conservative and highly specific enzymes capable of cleaving insoluble phytate compounds. In this review, we analyzed data on the properties of these enzymes, their differences from other phytases, and their unique spatial structures and substrate specificities. We considered influences of different factors on the catalytic activity and thermostability of these enzymes. There are few data on the hydrolysis mechanism of these enzymes, which makes it difficult to analyze their mechanism of action and their final products. We analyzed the available data on hydrolysis by β-propeller phytases of calcium complexes with myo-inositol hexakisphosphate.
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Affiliation(s)
- N P Balaban
- Kazan (Volga Region) Federal University, Kazan, 420008, Russia.
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15
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Sekula B, Ruszkowski M, Malinska M, Dauter Z. Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:350. [PMID: 27066023 PMCID: PMC4812014 DOI: 10.3389/fpls.2016.00350] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/07/2016] [Indexed: 05/17/2023]
Abstract
Putrescine, 1,4-diaminobutane, is an intermediate in the biosynthesis of more complexed polyamines, spermidine and spermine. Unlike other eukaryotes, plants have evolved a multistep pathway for putrescine biosynthesis that utilizes arginine. In the final reaction, N-carbamoylputrescine is hydrolyzed to putrescine by N-carbamoylputrescine amidohydrolase (CPA, EC 3.5.1.53). During the hydrolysis, consecutive nucleophilic attacks on the substrate by Cys158 and water lead to formation of putrescine and two by-products, ammonia and carbon dioxide. CPA from the model legume plant, Medicago truncatula (MtCPA), was investigated in this work. Four crystal structures were determined: the wild-type MtCPA in complex with the reaction intermediate, N-(dihydroxymethyl)putrescine as well as with cadaverine, which is a longer analog of putrescine; and also structures of MtCPA-C158S mutant unliganded and with putrescine. MtCPA assembles into octamers, which resemble an incomplete left-handed helical twist. The active site of MtCPA is funnel-like shaped, and its entrance is walled with a contribution of the neighboring protein subunits. Deep inside the catalytic cavity, Glu48, Lys121, and Cys158 form the catalytic triad. In this studies, we have highlighted the key residues, highly conserved among the plant kingdom, responsible for the activity and selectivity of MtCPA toward N-carbamoylputrescine. Moreover, since, according to previous reports, a close MtCPA relative from Arabidopsis thaliana, along with several other nitrilase-like proteins, are subjected to allosteric regulation by substrates, we have used the structural information to indicate a putative secondary binding site. Based on the docking experiment, we postulate that this site is adjacent to the entrance to the catalytic pocket.
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Affiliation(s)
- Bartosz Sekula
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of TechnologyLodz, Poland
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, ArgonneIL, USA
- *Correspondence: Milosz Ruszkowski,
| | - Maura Malinska
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, ArgonneIL, USA
- Faculty of Chemistry, University of WarsawWarsaw, Poland
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, ArgonneIL, USA
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16
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Alonso A, Pulido R. The extended human PTPome: a growing tyrosine phosphatase family. FEBS J 2015; 283:1404-29. [PMID: 26573778 DOI: 10.1111/febs.13600] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/02/2015] [Accepted: 11/13/2015] [Indexed: 12/13/2022]
Abstract
Tyr phosphatases are, by definition, enzymes that dephosphorylate phospho-Tyr (pTyr) from proteins. This activity is found in several structurally diverse protein families, including the protein Tyr phosphatase (PTP), arsenate reductase, rhodanese, haloacid dehalogenase (HAD) and His phosphatase (HP) families. Most of these families include members with substrate specificity for non-pTyr substrates, such as phospho-Ser/phospho-Thr, phosphoinositides, phosphorylated carbohydrates, mRNAs, or inorganic moieties. A Cys is essential for catalysis in PTPs, rhodanese and arsenate reductase enzymes, whereas this work is performed by an Asp in HAD phosphatases and by a His in HPs, via a catalytic mechanism shared by all of the different families. The category that contains most Tyr phosphatases is the PTP family, which, although it received its name from this activity, includes Ser, Thr, inositide, carbohydrate and RNA phosphatases, as well as some inactive pseudophosphatase proteins. Here, we propose an extended collection of human Tyr phosphatases, which we call the extended human PTPome. The addition of new members (SACs, paladin, INPP4s, TMEM55s, SSU72, and acid phosphatases) to the currently categorized PTP group of enzymes means that the extended human PTPome contains up to 125 proteins, of which ~ 40 are selective for pTyr. We set criteria to ascribe proteins to the extended PTPome, and summarize the more important features of the new PTPome members in the context of their phosphatase activity and their relationship with human disease.
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Affiliation(s)
- Andrés Alonso
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Rafael Pulido
- Biocruces Health Research Institute, Barakaldo, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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17
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Zeller E, Schollenberger M, Witzig M, Shastak Y, Kühn I, Hoelzle LE, Rodehutscord M. Interactions between supplemented mineral phosphorus and phytase on phytate hydrolysis and inositol phosphates in the small intestine of broilers
,. Poult Sci 2015; 94:1018-29. [DOI: 10.3382/ps/pev087] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2015] [Indexed: 11/20/2022] Open
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18
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Chen CC, Cheng KJ, Ko TP, Guo RT. Current Progresses in Phytase Research: Three-Dimensional Structure and Protein Engineering. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201400026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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19
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Graminho ER, Takaya N, Nakamura A, Hoshino T. Purification, biochemical characterization, and genetic cloning of the phytase produced by Burkholderia sp. strain a13. J GEN APPL MICROBIOL 2015; 61:15-23. [DOI: 10.2323/jgam.61.15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Takayuki Hoshino
- Faculty of Life and Environmental Sciences, University of Tsukuba
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20
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Weber S, Stirnimann CU, Wieser M, Frey D, Meier R, Engelhardt S, Li X, Capitani G, Kammerer RA, Hilbi H. A type IV translocated Legionella cysteine phytase counteracts intracellular growth restriction by phytate. J Biol Chem 2014; 289:34175-88. [PMID: 25339170 DOI: 10.1074/jbc.m114.592568] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The causative agent of Legionnaires' pneumonia, Legionella pneumophila, colonizes diverse environmental niches, including biofilms, plant material, and protozoa. In these habitats, myo-inositol hexakisphosphate (phytate) is prevalent and used as a phosphate storage compound or as a siderophore. L. pneumophila replicates in protozoa and mammalian phagocytes within a unique "Legionella-containing vacuole." The bacteria govern host cell interactions through the Icm/Dot type IV secretion system (T4SS) and ∼300 different "effector" proteins. Here we characterize a hitherto unrecognized Icm/Dot substrate, LppA, as a phytate phosphatase (phytase). Phytase activity of recombinant LppA required catalytically essential cysteine (Cys(231)) and arginine (Arg(237)) residues. The structure of LppA at 1.4 Å resolution revealed a mainly α-helical globular protein stabilized by four antiparallel β-sheets that binds two phosphate moieties. The phosphates localize to a P-loop active site characteristic of dual specificity phosphatases or to a non-catalytic site, respectively. Phytate reversibly abolished growth of L. pneumophila in broth, and growth inhibition was relieved by overproduction of LppA or by metal ion titration. L. pneumophila lacking lppA replicated less efficiently in phytate-loaded Acanthamoeba castellanii or Dictyostelium discoideum, and the intracellular growth defect was complemented by the phytase gene. These findings identify the chelator phytate as an intracellular bacteriostatic component of cell-autonomous host immunity and reveal a T4SS-translocated L. pneumophila phytase that counteracts intracellular bacterial growth restriction by phytate. Thus, bacterial phytases might represent therapeutic targets to combat intracellular pathogens.
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Affiliation(s)
- Stephen Weber
- From the Max von Pettenkofer Institute, Department of Medicine, Ludwig-Maximilians University Munich, 80336 Munich, Germany
| | - Christian U Stirnimann
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Mara Wieser
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Daniel Frey
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Roger Meier
- the Scientific Center for Optical and Electron Microscopy, ETH Zurich, 8093 Zurich, Switzerland
| | - Sabrina Engelhardt
- the Institute of Veterinary Physiology and Zurich Center for Integrative Human Physiology (ZIHP), Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland, and
| | - Xiaodan Li
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Guido Capitani
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Richard A Kammerer
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Hubert Hilbi
- From the Max von Pettenkofer Institute, Department of Medicine, Ludwig-Maximilians University Munich, 80336 Munich, Germany, the Institute of Medical Microbiology, Department of Medicine, University of Zurich, 8006 Zurich, Switzerland
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21
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Gruninger RJ, Thibault J, Capeness MJ, Till R, Mosimann SC, Sockett RE, Selinger BL, Lovering AL. Structural and biochemical analysis of a unique phosphatase from Bdellovibrio bacteriovorus reveals its structural and functional relationship with the protein tyrosine phosphatase class of phytase. PLoS One 2014; 9:e94403. [PMID: 24718691 PMCID: PMC3981807 DOI: 10.1371/journal.pone.0094403] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/14/2014] [Indexed: 11/19/2022] Open
Abstract
Bdellovibrio bacteriovorus is an unusual δ-proteobacterium that invades and preys on other Gram-negative bacteria and is of potential interest as a whole cell therapeutic against pathogens of man, animals and crops. PTPs (protein tyrosine phosphatases) are an important class of enzyme involved in desphosphorylating a variety of substrates, often with implications in cell signaling. The B. bacteriovorus open reading frame Bd1204 is predicted to encode a PTP of unknown function. Bd1204 is both structurally and mechanistically related to the PTP-like phytase (PTPLP) class of enzymes and possesses a number of unique properties not observed in any other PTPLPs characterized to date. Bd1204 does not display catalytic activity against some common protein tyrosine phosphatase substrates but is highly specific for hydrolysis of phosphomonoester bonds of inositol hexakisphosphate. The structure reveals that Bd1204 has the smallest and least electropositive active site of all characterized PTPLPs to date yet possesses a unique substrate specificity characterized by a strict preference for inositol hexakisphosphate. These two active site features are believed to be the most significant contributors to the specificity of phytate degrading enzymes. We speculate that Bd1204 may be involved in phosphate acquisition outside of prey.
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Affiliation(s)
- Robert J. Gruninger
- Lethbridge Research Center, Agriculture & Agri-Foods Canada, Lethbridge, AB, Canada
| | - John Thibault
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Michael J. Capeness
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Medical School, QMC, Nottingham, United Kingdom
| | - Robert Till
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Medical School, QMC, Nottingham, United Kingdom
| | - Steven C. Mosimann
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - R. Elizabeth Sockett
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Medical School, QMC, Nottingham, United Kingdom
| | - Brent L. Selinger
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Andrew L. Lovering
- Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail:
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22
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Rivera-Solís RA, Peraza-Echeverria S, Echevarría-Machado I, Herrera-Valencia VA. Chlamydomonas reinhardtii has a small family of purple acid phosphatase homologue genes that are differentially expressed in response to phytate. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0688-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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23
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Koveal D, Clarkson MW, Wood TK, Page R, Peti W. Ligand binding reduces conformational flexibility in the active site of tyrosine phosphatase related to biofilm formation A (TpbA) from Pseudomonasaeruginosa. J Mol Biol 2013; 425:2219-31. [PMID: 23524133 DOI: 10.1016/j.jmb.2013.03.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/06/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
Abstract
Tyrosine phosphatase related to biofilm formation A (TpbA) is a periplasmic dual-specificity phosphatase (DUSP) that controls biofilm formation in the pathogenic bacterium Pseudomonas aeruginosa. While DUSPs are known to regulate important cellular functions in both prokaryotes and eukaryotes, very few structures of bacterial DUSPs are available. Here, we present the solution structure of TpbA in the ligand-free open conformation, along with an analysis of the structural and dynamic changes that accompany ligand/phosphate binding. While TpbA adopts a typical DUSP fold, it also possesses distinct structural features that distinguish it from eukaryotic DUSPs. These include additional secondary structural elements, β0 and α6, and unique conformations of the variable insert, the α4-α5 loop and helix α5 that impart TpbA with a flat active-site surface. In the absence of ligand, the protein tyrosine phosphatase loop is disordered and the general acid loop adopts an open conformation, placing the catalytic aspartate, Asp105, more than 11Å away from the active site. Furthermore, the loops surrounding the active site experience motions on multiple timescales, consistent with a combination of conformational heterogeneity and fast (picosecond to nanosecond) timescale dynamics, which are significantly reduced upon ligand binding. Taken together, these data structurally distinguish TpbA and possibly other bacterial DUSPs from eukaryotic DUSPs and provide a rich picture of active-site dynamics in the ligand-free state that are lost upon ligand binding.
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Affiliation(s)
- Dorothy Koveal
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
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24
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Böhmer F, Szedlacsek S, Tabernero L, Ostman A, den Hertog J. Protein tyrosine phosphatase structure-function relationships in regulation and pathogenesis. FEBS J 2013; 280:413-31. [PMID: 22682070 DOI: 10.1111/j.1742-4658.2012.08655.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein phosphorylation on tyrosine residues is tightly controlled by protein tyrosine phosphatases (PTPs) at multiple levels: spatio-temporal expression, subcellular localization and post-translational modification. Structural and functional analysis of the PTP domains has provided insight into catalysis and regulatory mechanisms that control the enzymatic activity. Understanding the molecular basis of PTP regulation is of fundamental importance to dissect the pleiotropic effect of these enzymes in both health and disease. Here, we review recent insights into the regulation of receptor-like PTPs by extracellular ligands and into regulation by reversible oxidation that impairs catalysis directly. The physiological roles of PTPs are essential in homeostasis in eukaryotic cells and pertubation of their functional attributes causes different disease states. As an example, we discuss recent findings indicating how inappropriate oxidation of PTPs in cancer cells may contribute to cell transformation. On the other hand, PTPs from many pathogens are key virulence factors and manipulate signalling pathways in the host cells to promote invasion and survival of the microorganisms. This research area has received relatively little attention but has advanced remarkably. We review the structural features of pathogenic PTPs, their similarities and differences with eukaryotic PTPs, and the possible exploitation of this knowledge for therapeutic intervention.
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Affiliation(s)
- Frank Böhmer
- Center for Molecular Biomedicine, Jena University Hospital, Jena, Germany
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25
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Abstract
Phytases are phosphohydrolytic enzymes that initiate stepwise removal of phosphate from phytate. Simple-stomached species such as swine, poultry, and fish require extrinsic phytase to digest phytate, the major form of phosphorus in plant-based feeds. Consequently, this enzyme is supplemented in these species’ diets to decrease their phosphorus excretion, and it has emerged as one of the most effective and lucrative feed additives. This chapter provides a comprehensive review of the evolving course of phytase science and technology. It gives realistic estimates of the versatile roles of phytase in animal feeding, environmental protection, rock phosphorus preservation, human nutrition and health, and industrial applications. It elaborates on new biotechnology and existing issues related to developing novel microbial phytases as well as phytase-transgenic plants and animals. And it targets critical and integrated analyses on the global impact, novel application, and future demand of phytase in promoting animal agriculture, human health, and societal sustainability.
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Affiliation(s)
- Xin Gen Lei
- Department of Animal Science, Cornell University, Ithaca, New York 14853
| | | | | | | | - Michael J. Azain
- Department of Animal Science, University of Georgia, Athens, Georgia 30602
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26
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Gruninger RJ, Dobing S, Smith AD, Bruder LM, Selinger LB, Wieden HJ, Mosimann SC. Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases. J Biol Chem 2011; 287:9722-9730. [PMID: 22139834 DOI: 10.1074/jbc.m111.309872] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein-tyrosine phosphatase-like inositol polyphosphatases are microbial enzymes that catalyze the stepwise removal of one or more phosphates from highly phosphorylated myo-inositols via a relatively ordered pathway. To understand the substrate specificity and kinetic mechanism of these enzymes we have determined high resolution, single crystal, x-ray crystallographic structures of inactive Selenomonas ruminantium PhyA in complex with myo-inositol hexa- and pentakisphosphate. These structures provide the first glimpse of a myo-inositol polyphosphatase-ligand complex consistent with its known specificity and reveal novel features of the kinetic mechanism. To complement the structural studies, fluorescent binding assays have been developed and demonstrate that the K(d) for this enzyme is several orders of magnitude lower than the K(m). Together with rapid kinetics data, these results suggest that the protein tyrosine phosphatase-like inositol polyphosphatases have a two-step, substrate-binding mechanism that facilitates catalysis.
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Affiliation(s)
- Robert J Gruninger
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Selina Dobing
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Adam D Smith
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Lisza M Bruder
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - L Brent Selinger
- Departments of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Hans-Joachim Wieden
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Steven C Mosimann
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4.
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27
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Structural Analysis of a Multifunctional, Tandemly Repeated Inositol Polyphosphatase. J Mol Biol 2009; 392:75-86. [DOI: 10.1016/j.jmb.2009.05.079] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 05/26/2009] [Accepted: 05/28/2009] [Indexed: 11/21/2022]
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28
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Puhl AA, Greiner R, Selinger LB. Stereospecificity of myo-inositol hexakisphosphate hydrolysis by a protein tyrosine phosphatase-like inositol polyphosphatase from Megasphaera elsdenii. Appl Microbiol Biotechnol 2008; 82:95-103. [PMID: 18853154 DOI: 10.1007/s00253-008-1734-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 09/24/2008] [Accepted: 09/25/2008] [Indexed: 11/24/2022]
Abstract
Inositol polyphosphatases (IPPases), particularly those that can hydrolyze myo-inositol hexakisphosphate (Ins P(6)), are of biotechnological interest for their ability to reduce the metabolically unavailable organic phosphate content of feedstuffs and to produce lower inositol polyphosphates (IPPs) for research and pharmaceutical applications. Here, the gene coding for a new protein tyrosine phosphatase (PTP)-like IPPase was cloned from Megasphaera elsdenii (phyAme), and the biochemical properties of the recombinant protein were determined. The deduced amino acid sequence of PhyAme is similar to known PTP-like IPPases (29-44% identity), and the recombinant enzyme displayed strict specificity for IPP substrates. Optimal IPPase activity was displayed at an ionic strength of 250 mM, a pH of 5.0, and a temperature of 60 degrees C. In order to elucidate its stereospecificity of Ins P(6) dephosphorylation, a combination of high-performance ion-pair chromatography and kinetic studies was conducted. PhyAme displayed a stereospecificity that is unique among enzymes belonging to this class in that it preferentially cleaved Ins P(6) at one of two phosphate positions, 1D-3 or 1D-4. PhyAme followed two distinct and specific routes of hydrolysis, predominantly degrading Ins P(6) to Ins(2)P via: (a) 1D-Ins(1,2,4,5,6)P(5), 1D-Ins(1,2,5,6)P(4), 1D-Ins(1,2,6)P(3), and 1D-Ins(1,2)P(2) (60%) and (b) 1D-Ins(1,2,3,5,6)P(5), 1D-Ins(1,2,3,6)P(4), Ins(1,2,3)P(3), and D/L-Ins(1,2)P(2)(35%).
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Affiliation(s)
- Aaron A Puhl
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada
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Gruninger RJ, Selinger LB, Mosimann SC. Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr. FEBS J 2008; 275:3783-92. [PMID: 18573100 DOI: 10.1111/j.1742-4658.2008.06524.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protein tyrosine phosphatase (PTP)-like phytase, PhyAsr, from Selenomonas ruminantium is a novel member of the PTP superfamily, and the only described member that hydrolyzes myo-inositol-1,2,3,4,5,6-hexakisphosphate. In addition to the unique substrate specificity of PhyAsr, the phosphate-binding loop (P-loop) has been reported to undergo a conformational change from an open (inactive) to a closed (active) conformation upon ligand binding at low ionic strength. At high ionic strengths, the P-loop was observed in the closed, active conformation in both the presence and absence of ligand. To test whether the P-loop movement can be induced by changes in ionic strength, we examined the effect that ionic strength has on the catalytic efficiency of PhyAsr, and determined the structure of the enzyme at several ionic strengths. The catalytic efficiency of PhyAsr is highly sensitive to ionic strength, with a seven-fold increase in k(cat)/K(m) and a ninefold decrease in K(m) when the ionic strength is increased from 100 to 500 mm. Surprisingly, the P-loop is observed in the catalytically competent conformation at all ionic strengths, despite the absence of a ligand. Here we provide structural evidence that the ionic strength dependence of PhyAsr and the conformational change in the P-loop are not linked. Furthermore, we demonstrate that the previously reported P-loop conformational change is a result of irreversible oxidation of the active site thiolate. Finally, we rationalize the observed P-loop conformational changes observed in all oxidized PTP structures.
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Affiliation(s)
- Robert J Gruninger
- Department of Chemistry and Biochemistry, University of Lethbridge, Canada
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30
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Puhl AA, Greiner R, Selinger LB. Kinetics, substrate specificity, and stereospecificity of two new protein tyrosine phosphatase-like inositol polyphosphatases from Selenomonas lacticifex. Biochem Cell Biol 2008; 86:322-30. [DOI: 10.1139/o08-095] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Inositol polyphosphatases (IPPases) play an important role in the metabolism of inositol polyphosphates, a class of molecules involved in signal transduction. Here we characterize 2 new protein tyrosine phosphatase-like IPPases (PhyAsl and PhyBsl) cloned from Selenomonas lacticifex that can hydrolyze myo-inositol hexakisphosphate (InsP6) in vitro. To determine their preferred substrates and stereospecificity of InsP6 dephosphorylation, a combination of kinetic and high-performance ion pair chromatography studies were conducted. Despite only 33% amino acid sequence identity between them, both enzymes display strict specificity for IPP substrates and cleave InsP6 primarily at the d-3-phosphate position (>90%). Furthermore, both enzymes predominantly degrade InsP6 to Ins(2)P via identical and very specific routes of dephosphorylation (3,4,5,6,1). Despite these similarities, PhylAsl is shown to have a slight kinetic preference for the major inositol pentakisphosphate intermediate in its InsP6 hydrolysis pathway, whereas PhyBsl displays a unique and substantial preference for an inositol tetrakisphosphate intermediate.
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Affiliation(s)
- Aaron A. Puhl
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Microbiology and Biotechnology, Max Rubner Institute, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - Ralf Greiner
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Microbiology and Biotechnology, Max Rubner Institute, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - L. Brent Selinger
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Microbiology and Biotechnology, Max Rubner Institute, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
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31
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Puhl AA, Greiner R, Selinger LB. A protein tyrosine phosphatase-like inositol polyphosphatase from Selenomonas ruminantium subsp. lactilytica has specificity for the 5-phosphate of myo-inositol hexakisphosphate. Int J Biochem Cell Biol 2008; 40:2053-64. [DOI: 10.1016/j.biocel.2008.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 01/18/2008] [Accepted: 02/10/2008] [Indexed: 11/28/2022]
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