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Winkler KF, Panse L, Maiwald C, Hayeß J, Fischer P, Fehlau M, Neubauer P, Kurreck A. Screening the Thermotoga maritima genome for new wide-spectrum nucleoside and nucleotide kinases. J Biol Chem 2023:104746. [PMID: 37094698 DOI: 10.1016/j.jbc.2023.104746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/12/2023] [Accepted: 04/16/2023] [Indexed: 04/26/2023] Open
Abstract
Enzymes from thermophilic organisms are interesting biocatalysts for a wide variety of applications in organic synthesis, biotechnology and molecular biology. Next to an increased stability at elevated temperatures, they were described to show a wider substrate spectrum than their mesophilic counterparts. To identify thermostable biocatalysts for the synthesis of nucleotide analogs, we performed a database search on the carbohydrate and nucleotide metabolism of T. maritima. After expression and purification of 13 enzyme candidates involved in nucleotide synthesis, these enzymes were screened for their substrate scope. We found that the synthesis of 2'-deoxynucleoside 5'-monophosphates (dNMPs) and uridine 5'-monophosphate from nucleosides was catalyzed by the already known wide-spectrum thymidine kinase (TK) and the ribokinase. In contrast, no NMP-forming activity was detected for adenosine-specific kinase, uridine kinase or nucleotidase. The NMP kinases (NMPKs) and the pyruvate-phosphate-dikinase of T. maritima exhibited a rather specific substrate spectrum for the phosphorylation of NMPs, while pyruvate kinase, acetate kinase and three of the NMPKs showed a broad substrate scope with (2'-deoxy)nucleoside 5'-diphosphates as substrates. Based on these promising results, TmNMPKs were applied in enzymatic cascade reactions for nucleoside 5'-triphosphate synthesis using four modified pyrimidine nucleosides and four purine NMPs as substrates, and we determined that base- and sugar-modified substrates were accepted. In summary, besides the already reported TmTK, NMPKs of T. maritima were identified to be interesting enzyme candidates for the enzymatic production of modified nucleotides.
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Affiliation(s)
- Katja F Winkler
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | - Lena Panse
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | | | - Josefine Hayeß
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | - Pascal Fischer
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | - Maryke Fehlau
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany; BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany
| | - Peter Neubauer
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany
| | - Anke Kurreck
- Technische Universität Berlin, Faculty III Process Sciences, Institute of Biotechnology, Chair of Bioprocess Engineering, Ackerstraße 76, 13355 Berlin, Germany; BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
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Tomoike F, Tsunetou A, Kim K, Nakagawa N, Kuramitsu S, Masui R. A putative adenosine kinase family protein possesses adenosine diphosphatase activity. Biosci Biotechnol Biochem 2016; 80:2138-2143. [PMID: 27484886 DOI: 10.1080/09168451.2016.1214532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Adenosine kinase is a potential target for development of new types of drugs. The COG1839 family has been defined as "adenosine-specific kinase" family based on structural analysis and the adenosine-binding ability of a family member, PAE2307. However, there has been no experimental evidence with regard to the enzymatic function of this protein family. Here we measured the enzymatic activity of TTHA1091, a COG1839 family protein from Thermus thermophilus HB8. The phosphorylation of adenosine by TTHA1091 was undetectable when ATP or ADP were used as phosphate donor. However, the degradation of ADP to AMP was detected, indicating that this protein possessed adenosine diphosphatase (ADPase) activity. The (ADPase) activity was inhibited by divalent cations and was specific to ADP and CDP. Thus, this study provides the first experimental evidence for the enzymatic function of the "adenosine-specific kinase" family and suggests a need to reexamine its functional annotation.
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Affiliation(s)
- Fumiaki Tomoike
- a Graduate School of Frontier Biosciences , Osaka University , Suita , Osaka , Japan.,b Research Center for Materials Science , Nagoya University , Nagoya, Aichi , Japan
| | - Akiko Tsunetou
- c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan
| | - Kwang Kim
- c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan
| | - Noriko Nakagawa
- c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan
| | - Seiki Kuramitsu
- a Graduate School of Frontier Biosciences , Osaka University , Suita , Osaka , Japan.,c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan
| | - Ryoji Masui
- c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan.,d Graduate School of Science , Osaka City University , Osaka , Japan
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Wieland T, Attwood PV. Alterations in reversible protein histidine phosphorylation as intracellular signals in cardiovascular disease. Front Pharmacol 2015; 6:173. [PMID: 26347652 PMCID: PMC4543942 DOI: 10.3389/fphar.2015.00173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/03/2015] [Indexed: 01/27/2023] Open
Abstract
Reversible phosphorylation of amino acid side chains in proteins is a frequently used mechanism in cellular signal transduction and alterations of such phosphorylation patterns are very common in cardiovascular diseases. They reflect changes in the activities of the protein kinases and phosphatases involving signaling pathways. Phosphorylation of serine, threonine, and tyrosine residues has been extensively investigated in vertebrates, whereas reversible histidine phosphorylation, a well-known regulatory signal in lower organisms, has been largely neglected as it has been generally assumed that histidine phosphorylation is of minor importance in vertebrates. More recently, it has become evident that the nucleoside diphosphate kinase isoform B (NDPK-B), an ubiquitously expressed enzyme involved in nucleotide metabolism, and a highly specific phosphohistidine phosphatase (PHP) form a regulatory histidine protein kinase/phosphatase system in mammals. At least three well defined substrates of NDPK-B are known: The β-subunit of heterotrimeric G-proteins (Gβ), the intermediate conductance potassium channel SK4 and the Ca(2+) conducting TRP channel family member, TRPV5. In each of these proteins the phosphorylation of a specific histidine residue regulates cellular signal transduction or channel activity. This article will therefore summarize our current knowledge on protein histidine phosphorylation and highlight its relevance for cardiovascular physiology and pathophysiology.
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Affiliation(s)
- Thomas Wieland
- Institute for Experimental and Clinical Pharmacology and Toxicology, Mannheim Medical Faculty, Heidelberg University , Mannheim, Germany
| | - Paul V Attwood
- School of Chemistry and Biochemistry, The University of Western Australia , Crawley, Australia
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Styrene is sensed by the N-terminal PAS sensor domain of StyS, a double sensor kinase from the styrene-degrading bacterium Pseudomonas fluorescens ST. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0931-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Takahata Y, Inoue M, Kim K, Iio Y, Miyamoto M, Masui R, Ishihama Y, Kuramitsu S. Close proximity of phosphorylation sites to ligand in the phosphoproteome of the extreme thermophile Thermus thermophilus
HB8. Proteomics 2012; 12:1414-30. [DOI: 10.1002/pmic.201100573] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yoshio Takahata
- Graduate School of Frontier Biosciences; Osaka University; Osaka Japan
| | - Masao Inoue
- Department of Biological Sciences; Graduate School of Science; Osaka University; Osaka Japan
| | - Kwang Kim
- Department of Biological Sciences; Graduate School of Science; Osaka University; Osaka Japan
| | - Yota Iio
- Department of Biological Sciences; Graduate School of Science; Osaka University; Osaka Japan
| | - Masaaki Miyamoto
- Radio Isotope Division; Center for Supports to Research and Education Activities; Department of Biology; Graduate School of Science; Kobe University; Kobe Japan
| | - Ryoji Masui
- Department of Biological Sciences; Graduate School of Science; Osaka University; Osaka Japan
- RIKEN SPring-8 Center; 1-1-1 Kouto Sayo-cho, Sayo-gun Hyogo Japan
| | - Yasushi Ishihama
- Institute for Advanced Biosciences; Keio University; Yamagata Japan
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto Japan
| | - Seiki Kuramitsu
- Graduate School of Frontier Biosciences; Osaka University; Osaka Japan
- Department of Biological Sciences; Graduate School of Science; Osaka University; Osaka Japan
- RIKEN SPring-8 Center; 1-1-1 Kouto Sayo-cho, Sayo-gun Hyogo Japan
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Trajtenberg F, Graña M, Ruétalo N, Botti H, Buschiazzo A. Structural and enzymatic insights into the ATP binding and autophosphorylation mechanism of a sensor histidine kinase. J Biol Chem 2010; 285:24892-903. [PMID: 20507988 PMCID: PMC2915725 DOI: 10.1074/jbc.m110.147843] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Indexed: 11/06/2022] Open
Abstract
DesK is a sensor histidine kinase (HK) that allows Bacillus subtilis to respond to cold shock, triggering the adaptation of membrane fluidity via transcriptional control of a fatty acid desaturase. It belongs to the HK family HPK7, which includes the nitrogen metabolism regulators NarX/Q and the antibiotic sensor LiaS among other important sensor kinases. Structural information on different HK families is still scarce and several questions remain, particularly concerning the molecular features that determine HK specificity during its catalytic autophosphorylation and subsequent response-regulator phosphotransfer reactions. To analyze the ATP-binding features of HPK7 HKs and dissect their mechanism of autophosphorylation at the molecular level, we have studied DesK in complex with ATP using high resolution structural approaches in combination with biochemical studies. We report the first crystal structure of an HK in complex with its natural nucleotidic substrate. The general fold of the ATP-binding domain of DesK is conserved, compared with well studied members of other families. Yet, DesK displays a far more compact structure at the ATP-binding pocket: the ATP lid loop is much shorter with no secondary structural organization and becomes ordered upon ATP loading. Sequence conservation mapping onto the molecular surface, semi-flexible protein-protein docking simulations, and structure-based point mutagenesis allow us to propose a specific domain-domain geometry during autophosphorylation catalysis. Supporting our hypotheses, we have been able to trap an autophosphorylating intermediate state, by protein engineering at the predicted domain-domain interaction surface.
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Affiliation(s)
| | - Martin Graña
- Bioinformatics, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay and
| | | | | | - Alejandro Buschiazzo
- From the Units of Protein Crystallography and
- the Department of Structural Biology and Chemistry, Institut Pasteur, Paris 75015, France
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Sharpe ML, Gao C, Kendall SL, Baker EN, Lott JS. The Structure and Unusual Protein Chemistry of Hypoxic Response Protein 1, a Latency Antigen and Highly Expressed Member of the DosR Regulon in Mycobacterium tuberculosis. J Mol Biol 2008; 383:822-36. [DOI: 10.1016/j.jmb.2008.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 06/30/2008] [Accepted: 07/02/2008] [Indexed: 01/20/2023]
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Baker EN. Structural genomics as an approach towards understanding the biology of tuberculosis. ACTA ACUST UNITED AC 2007; 8:57-65. [PMID: 17668294 DOI: 10.1007/s10969-007-9020-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 07/09/2007] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) is a devastating disease of worldwide importance. The availability of the genome sequence of Mycobacterium tuberculosis (Mtb), the causative agent, has stimulated a large variety of genome-scale initiatives. These include international structural genomics efforts which have the dual aim of characterising potential new drug targets and addressing key aspects of the biology of Mtb. This review highlights the various ways in which structural analysis has illuminated the biological activities of Mtb gene products, which were previously of unknown or uncertain function. Key information comes from the protein fold, from bound ligands, solvent molecules, ions etc. or from unexpectedly modified amino acid residues. Most importantly, the three dimensional structure of a protein permits the integration of data from many sources, both bioinformatic and experimental, to develop testable functional hypotheses. This has led to many new insights into TB biology.
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Affiliation(s)
- Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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Puttick J, Baker EN, Delbaere LTJ. Histidine phosphorylation in biological systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1784:100-5. [PMID: 17728195 DOI: 10.1016/j.bbapap.2007.07.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 07/14/2007] [Accepted: 07/17/2007] [Indexed: 10/23/2022]
Abstract
Histidine phosphorylation is important in prokaryotes and occurs to the extent of 6% of total phosphorylation in eukaryotes. Nevertheless phosphohistidine residues are not normally observed in proteins due to rapid hydrolysis of the phosphoryl group under acidic conditions. Many rapid processes employ phosphohistidines, including the bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS), the bacterial two-component systems and reactions catalyzed by enzymes such as nucleoside diphosphate kinase and succinyl-CoA synthetase. In the PTS, the NMR structure of the phosphohistidine moiety of the phosphohistidine-containing protein was determined but no X-ray structures of phosphohistidine forms of PTS proteins have been elucidated. There have been crystal structures of a few phosphohistidine-containing proteins determined: nucleoside diphosphate kinase, succinyl-CoA synthetase, a cofactor-dependent phosphoglycerate mutase and the protein PAE2307 from the hyperthermophilic archaeon Pyrobaculum aerophilum. A common theme for these stable phosphohistidines is the occurrence of ion-pair hydrogen bonds (salt bridges) involving the non-phosphorylated nitrogen atom of the histidine imidazole ring with an acidic amino acid side chain.
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Affiliation(s)
- Jennifer Puttick
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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