1
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Expression of adenylate kinase fused MEK1R4F in Escherichia coli and its application in ERK phosphorylation. Biotechnol Lett 2017; 39:1553-1558. [PMID: 28748350 DOI: 10.1007/s10529-017-2385-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 06/22/2017] [Indexed: 01/29/2023]
Abstract
OBJECTIVE To construct a highly expressed and active MEK1R4F (a constitutively active form of mitogen-activated protein kinase kinase 1) by fusion of soluble adenylate kinase (Adk) tag, resulting in Adk-MEK1R4F protein suitable for preparation of phosphorylated ERK. RESULTS We fused the Adk to the N-terminus of MEK1R4F through overlapping PCR. The expression of Adk-MEK1R4F fusion protein increased ~10-fold in Escherichia coli, and was purified to 95% via two purification steps including Ni-NTA and Q Sepharose fast flow (QFF) chromatography. The purified Adk-MEK1R4F protein was functional for ERK phosphorylation and could use ADP in addition to ATP. The Adk-MEK1R4F had higher catalytic activity than regular MEK1R4F both in vitro and in cell-free extracts system. CONCLUSIONS Adenylate kinase was used as a soluble tag to facilitate MEK1R4F protein expression and its application in large-scale phosphorylated ERK1/2 preparation and purification.
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2
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Luo D, Wen C, Zhao R, Liu X, Liu X, Cui J, Liang JG, Liang P. High Level Expression and Purification of Recombinant Proteins from Escherichia coli with AK-TAG. PLoS One 2016; 11:e0156106. [PMID: 27214237 PMCID: PMC4877045 DOI: 10.1371/journal.pone.0156106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/08/2016] [Indexed: 01/01/2023] Open
Abstract
Adenylate kinase (AK) from Escherichia coli was used as both solubility and affinity tag for recombinant protein production. When fused to the N-terminus of a target protein, an AK fusion protein could be expressed in soluble form and purified to near homogeneity in a single step from Blue-Sepherose via affinity elution with micromolar concentration of P1, P5- di (adenosine—5’) pentaphosphate (Ap5A), a transition-state substrate analog of AK. Unlike any other affinity tags, the level of a recombinant protein expression in soluble form and its yield of recovery during each purification step could be readily assessed by AK enzyme activity in near real time. Coupled to a His-Tag installed at the N-terminus and a thrombin cleavage site at the C terminus of AK, the streamlined method, here we dubbed AK-TAG, could also allow convenient expression and retrieval of a cleaved recombinant protein in high yield and purity via dual affinity purification steps. Thus AK-TAG is a new addition to the arsenal of existing affinity tags for recombinant protein expression and purification, and is particularly useful where soluble expression and high degree of purification are at stake.
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Affiliation(s)
- Dan Luo
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Caixia Wen
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Rongchuan Zhao
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Xinyu Liu
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Xinxin Liu
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Jingjing Cui
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | | | - Peng Liang
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
- Clover Biopharmaceuticals, Chengdu, China
- GenHunter Corporation, Grassmere Park, Nashville, United States of America
- * E-mail: ;
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3
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Use of adenylate kinase as a solubility tag for high level expression of T4 DNA ligase in Escherichia coli. Protein Expr Purif 2015; 109:79-84. [PMID: 25700573 DOI: 10.1016/j.pep.2015.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 11/20/2022]
Abstract
The discovery of T4 DNA ligase in 1960s was pivotal in the spread of molecular biotechnology. The enzyme has become ubiquitous for recombinant DNA routinely practiced in biomedical research around the globe. Great efforts have been made to express and purify T4 DNA ligase to meet the world demand, yet over-expression of soluble T4 DNA ligase in E. coli has been difficult. Here we explore the use of adenylate kinase to enhance T4 DNA ligase expression and its downstream purification. E.coli adenylate kinase, which can be expressed in active form at high level, was fused to the N-terminus of T4 DNA ligase. The resulting His-tagged AK-T4 DNA ligase fusion protein was greatly over-expressed in E. coli, and readily purified to near homogeneity via two purification steps consisting of Blue Sepharose and Ni-NTA chromatography. The purified AK-T4 DNA ligase not only is fully active for DNA ligation, but also can use ADP in addition to ATP as energy source since adenylate kinase converts ADP to ATP and AMP. Thus adenylate kinase may be used as a solubility tag to facilitate recombinant protein expression as well as their downstream purification.
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4
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Zhou Y, Asahara H, Gaucher EA, Chong S. Reconstitution of translation from Thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components. Nucleic Acids Res 2012; 40:7932-45. [PMID: 22723376 PMCID: PMC3439929 DOI: 10.1093/nar/gks568] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Thermus thermophilus is a thermophilic model organism distantly related to the mesophilic model organism E. coli. We reconstituted protein translation of Thermus thermophilus in vitro from purified ribosomes, transfer ribonucleic acids (tRNAs) and 33 recombinant proteins. This reconstituted system was fully functional, capable of translating natural messenger RNA (mRNA) into active full-length proteins at temperatures up to 65°C and with yields up to 60 μg/ml. Surprisingly, the synthesis of active proteins also occurred at 37°C, a temperature well below the minimal growth temperature for T. thermophilus. A polyamine was required, with tetraamine being most effective, for translation at both high and low temperatures. Using such a defined in vitro system, we demonstrated a minimal set of components that are sufficient for synthesizing active proteins at high temperatures, the functional compatibility of key translation components between T. thermophilus and E. coli, and the functional conservation of a number of resurrected ancient elongation factors. This work sets the stage for future experiments that apply abundant structural information to biochemical characterization of protein translation and folding in T. thermophilus. Because it contains significantly reduced nucleases and proteases, this reconstituted thermostable cell-free protein synthesis system may enable in vitro engineering of proteins with improved thermostability.
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Affiliation(s)
- Ying Zhou
- New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
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5
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Zinc-, cobalt- and iron-chelated forms of adenylate kinase from the Gram-negative bacterium Desulfovibrio gigas. Int J Biol Macromol 2009; 45:524-31. [DOI: 10.1016/j.ijbiomac.2009.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 09/18/2009] [Indexed: 11/19/2022]
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6
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Gavel OY, Bursakov SA, Di Rocco G, Trincão J, Pickering IJ, George GN, Calvete JJ, Shnyrov VL, Brondino CD, Pereira AS, Lampreia J, Tavares P, Moura JJG, Moura I. A new type of metal-binding site in cobalt- and zinc-containing adenylate kinases isolated from sulfate-reducers Desulfovibrio gigas and Desulfovibrio desulfuricans ATCC 27774. J Inorg Biochem 2008; 102:1380-95. [PMID: 18328566 DOI: 10.1016/j.jinorgbio.2008.01.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 01/13/2008] [Accepted: 01/18/2008] [Indexed: 11/28/2022]
Abstract
Adenylate kinase (AK) mediates the reversible transfer of phosphate groups between the adenylate nucleotides and contributes to the maintenance of their constant cellular level, necessary for energy metabolism and nucleic acid synthesis. The AK were purified from crude extracts of two sulfate-reducing bacteria (SRB), Desulfovibrio (D.) gigas NCIB 9332 and Desulfovibrio desulfuricans ATCC 27774, and biochemically and spectroscopically characterised in the native and fully cobalt- or zinc-substituted forms. These are the first reported adenylate kinases that bind either zinc or cobalt and are related to the subgroup of metal-containing AK found, in most cases, in Gram-positive bacteria. The electronic absorption spectrum is consistent with tetrahedral coordinated cobalt, predominantly via sulfur ligands, and is supported by EPR. The involvement of three cysteines in cobalt or zinc coordination was confirmed by chemical methods. Extended X-ray absorption fine structure (EXAFS) indicate that cobalt or zinc are bound by three cysteine residues and one histidine in the metal-binding site of the "LID" domain. The sequence 129Cys-X5-His-X15-Cys-X2-Cys of the AK from D. gigas is involved in metal coordination and represents a new type of binding motif that differs from other known zinc-binding sites of AK. Cobalt and zinc play a structural role in stabilizing the LID domain.
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Affiliation(s)
- Olga Yu Gavel
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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7
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Cannabidiolic-acid synthase, the chemotype-determining enzyme in the fiber-type Cannabis sativa. FEBS Lett 2007; 581:2929-34. [PMID: 17544411 DOI: 10.1016/j.febslet.2007.05.043] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 05/15/2007] [Indexed: 11/21/2022]
Abstract
Cannabidiolic-acid (CBDA) synthase is the enzyme that catalyzes oxidative cyclization of cannabigerolic-acid into CBDA, the dominant cannabinoid constituent of the fiber-type Cannabis sativa. We cloned a novel cDNA encoding CBDA synthase by reverse transcription and polymerase chain reactions with degenerate and gene-specific primers. Biochemical characterization of the recombinant enzyme demonstrated that CBDA synthase is a covalently flavinylated oxidase. The structural and functional properties of CBDA synthase are quite similar to those of tetrahydrocannabinolic-acid (THCA) synthase, which is responsible for the biosynthesis of THCA, the major cannabinoid in drug-type Cannabis plants.
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8
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Ravera S, Musante L, Calzia D, Panfoli I, Bruschi M, Candiano G, Pepe IM, Morelli A. Expression of adenylate kinase 1 in bovine retinal cytosol. Curr Eye Res 2007; 32:249-57. [PMID: 17453945 DOI: 10.1080/02713680601161212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Adenylate kinases (AKs) are ubiquitous phosphotransferases that contribute to homeostasis of adenine nucleotide composition in cells. Six AK isoforms were found in vertebrates. We report that soluble AK isoform 1 is expressed in the cytosol of bovine retina consistently devoid of rod outer segments. Immunoblotting analysis with a polyclonal antibody raised against soluble adenylate kinase and subsequent sequencing of eluted peptide by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry allowed enzyme isolation by joining purification methods to two-dimensional electrophoresis. In this study, we found that cytosolic adenylate kinase isoform 1 is expressed in bovine retina. Cytoplasmic AK1 would physiologically contribute to retinal energy metabolism.
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Affiliation(s)
- Silvia Ravera
- Biology Department, University of Genoa, Genova, Italy
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9
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Ravera S, Calzia D, Panfoli I, Pepe IM, Morelli A. Simultaneous detection of molecular weight and activity of adenylate kinases after electrophoretic separation. Electrophoresis 2007; 28:291-300. [PMID: 17203507 DOI: 10.1002/elps.200600353] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adenylate kinases (AKs) are ubiquitous monomeric phosphotransferases catalyzing the reversible reaction, AMP + MgATP = ADP + MgADP, which plays a pivotal role in the energetic metabolism. In vertebrates, six AK isoforms are known. In this work, we report the detection of many AK isoforms directly on gel or NC after separation by denaturing electrophoresis and electroblotting, by an optimized protocol for the enzyme detection. The method allows to clarify the apparent MW of most of those AK isozymes that follow the cited reaction, especially onto NC where bands are sharper due to the absence of protein diffusion. In contrast, GTP:AMP phosphotransferases are not detectable. AK activity from many sources can be detected in both its reaction courses; ATP production appears as dark-blue bands, while ADP formation appears as nonfluorescent bands over a fluorescent background, under long-wavelength UV light. We show that nondenaturing gel electrophoresis is not the first choice for AK activity detection. Our method is different from the preceding reports on AK activity detection in bacteria after native polyacrylamide gel separations, in the absence of SDS or methanol. The procedure is also quantitative, allowing to determine the amount of enzyme present in samples.
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Affiliation(s)
- Silvia Ravera
- Department of Biology, University of Genoa, Genova, Italy.
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10
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Hible G, Christova P, Renault L, Seclaman E, Thompson A, Girard E, Munier-Lehmann H, Cherfils J. Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase. Proteins 2006; 62:489-500. [PMID: 16288457 DOI: 10.1002/prot.20662] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Bacterial nucleoside monophosphate (NMP) kinases, which convert NMPs to nucleoside diphosphates (NDP), are investigated as potential antibacterial targets against pathogenic bacteria. Herein, we report the biochemical and structural characterization of GMP kinase from Mycobacterium tuberculosis (GMPKMt). GMPKMt is a monomer with an unusual specificity for ATP as a phosphate donor, a lower catalytic efficiency compared with eukaryotic GMPKs, and it carries two redox-sensitive cysteines in the central CORE domain. These properties were analyzed in the light of the high-resolution crystal structures of unbound, GMP-bound, and GDP-bound GMPKMt. The latter structure was obtained in both an oxidized form, in which the cysteines form a disulfide bridge, and a reduced form which is expected to correspond to the physiological enzyme. GMPKMt has a modular domain structure as most NMP kinases. However, it departs from eukaryotic GMPKs by the unusual conformation of its CORE domain, and by its partially open LID and GMP-binding domains which are the same in the apo-, GMP-bound, and GDP-bound forms. GMPKMt also features a unique GMP binding site which is less close-packed than that of mammalian GMPKs, and in which the replacement of a critical tyrosine by a serine removes a catalytic interaction. In contrast, the specificity of GMPKMt for ATP may be a general feature of GMPKs because of an invariant structural motif that recognizes the adenine base. Altogether, differences in domain dynamics and GMP binding between GMPKMt and mammalian GMPKs should reveal clues for the design of GMPKMt-specific inhibitors.
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Affiliation(s)
- Guillaume Hible
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France
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11
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Hible G, Renault L, Schaeffer F, Christova P, Zoe Radulescu A, Evrin C, Gilles AM, Cherfils J. Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase. J Mol Biol 2005; 352:1044-59. [PMID: 16140325 DOI: 10.1016/j.jmb.2005.07.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 07/11/2005] [Accepted: 07/14/2005] [Indexed: 10/25/2022]
Abstract
Guanosine monophosphate kinases (GMPKs), which catalyze the phosphorylation of GMP and dGMP to their diphosphate form, have been characterized as monomeric enzymes in eukaryotes and prokaryotes. Here, we report that GMPK from Escherichia coli (ecGMPK) assembles in solution and in the crystal as several different oligomers. Thermodynamic analysis of ecGMPK using differential scanning calorimetry shows that the enzyme is in equilibrium between a dimer and higher order oligomers, whose relative amounts depend on protein concentration, ionic strength, and the presence of ATP. Crystallographic structures of ecGMPK in the apo, GMP and GDP-bound forms were solved at 3.2A, 2.9A and 2.4A resolution, respectively. ecGMPK forms a hexamer with D3 symmetry in all crystal forms, in which the two nucleotide-binding domains are able to undergo closure comparable to that of monomeric GMPKs. The 2-fold and 3-fold interfaces involve a 20-residue C-terminal extension and a sequence signature, respectively, that are missing from monomeric eukaryotic GMPKs, explaining why ecGMPK forms oligomers. These signatures are found in GMPKs from proteobacteria, some of which are human pathogens. GMPKs from these bacteria are thus likely to form the same quaternary structures. The shift of the thermodynamic equilibrium towards the dimer at low ecGMPK concentration together with the observation that inter-subunit interactions partially occlude the ATP-binding site in the hexameric structure suggest that the dimer may be the active species at physiological enzyme concentration.
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Affiliation(s)
- Guillaume Hible
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette 91198, France
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12
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Gavel OY, Bursakov SA, Pina DG, Zhadan GG, Moura JJG, Moura I, Shnyrov VL. Structural stability of adenylate kinase from the sulfate-reducing bacteria Desulfovibrio gigas. Biophys Chem 2005; 110:83-92. [PMID: 15223146 DOI: 10.1016/j.bpc.2004.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Revised: 01/21/2004] [Accepted: 01/22/2004] [Indexed: 11/17/2022]
Abstract
A novel adenylate kinase (AK) has recently been purified from Desulfovibrio gigas and characterized as a Co(2+)/Zn(2+)-containing enzyme: this is an unusual characteristic for AKs from Gram-negative bacteria, in which these enzymes are normally devoid of metals. Here, we studied the conformational stability of holo- and apo-AK as a function of temperature by differential scanning calorimetry (DSC), circular dichroism (CD), and intrinsic fluorescence spectroscopy. The thermal unfolding of AK is a cooperative two-state process, and is sufficiently reversible in the 9-11 pH range, that can be correctly interpreted in terms of a simple two-state thermodynamic model. The spectral parameters as monitored by ellipticity changes in the CD spectra of the enzyme as well as the decrease in tryptophan intensity emission upon heating were seen to be good complements to the highly sensitive but integral DSC-method.
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Affiliation(s)
- Olga Yu Gavel
- Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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13
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Hibino T. Nonfixed relationship of the Michaelis constant and maximum velocity with their corresponding rate constants. J Biol Chem 2005; 280:30671-80. [PMID: 15972825 DOI: 10.1074/jbc.m412601200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Michaelis constant (K(m)) and V(mas) (E0k(cat)) values for two mutant sets of enzymes were studied from the viewpoint of their definition in a rapid equilibrium reaction model and in a steady state reaction model. The "AMP set enzyme" had a mutation at the AMP-binding site (Y95F, V67I, and V67I/L76V), and the "ATP set enzyme" had a mutation at a possible ATP-binding region (Y32F, Y34F, and Y32A/Y34A). Reaction rate constants obtained using steady state model analysis explained discrepancies found by the rapid equilibrium model analysis. (i) The unchanged number of bound AMPs for Y95F and the wild type despite the markedly increased K(m) values for AMP of the AMP set of enzymes was explained by alteration of the rate constants of the AMP step (k(+2), k(-2)) to retain the ratio k(+2)/k(-2). (ii) A 100 times weakened selectivity of ATP for Y34F in contrast to no marked changes in K(m) values for both ATP and AMP for the ATP set of enzymes was explained by the alteration of the rate constants of the ATP steps. A similar alteration of the K(m) and k(cat) values of these enzymes resulted from distinctive alterations of their rate constants. The pattern of alteration was highly suggestive. The most interesting finding was that the rate constants that decided the K(m) and k(cat) values were replaced by the mutation, and the simple relationships between K(m), k(cat), and the rate constants of K(m)1 = k(+1)/k(-1) and k(cat) = k(f) were not valid. The nature of the K(m) and k(cat) alterations was discussed.
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Affiliation(s)
- Takeshi Hibino
- Laboratory of Biophysical Chemistry, Graduate School of Agriculture and Biological Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
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14
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Ravera S, Repaci E, Morelli A, Pepe IM, Botter R, Beruto D. Effects of extremely low frequency electromagnetic fields on the adenylate kinase activity of rod outer segment of bovine retina. Bioelectromagnetics 2005; 25:545-51. [PMID: 15376242 DOI: 10.1002/bem.20031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Extremely low frequency electromagnetic fields (ELF-EMFs) of 75 Hz with amplitudes above a threshold of about 125 microT have a dramatic effect on the adenylate kinase (AK) activity of the rod outer segment (ROS) membranes. In fact, the ATP production by ROS membranes or by purified disk membranes placed in the field decreased by approximately 54%. The decrease in enzymatic activity was independent of the time of exposure to the field and was completely reversible. When disk membranes were solubilized with Triton or a soluble isoform of AK was used, negligible effects of the field were obtained on the enzymatic activity, suggesting that the membrane has an important role in determining the conditions for the enzyme inactivation.
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Affiliation(s)
- S Ravera
- Department of DIBISAA, University of Genoa, Genoa, Italy
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15
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Couñago R, Shamoo Y. Gene replacement of adenylate kinase in the gram-positive thermophile Geobacillus stearothermophilus disrupts adenine nucleotide homeostasis and reduces cell viability. Extremophiles 2005; 9:135-44. [PMID: 15647886 DOI: 10.1007/s00792-004-0428-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Accepted: 10/25/2004] [Indexed: 11/28/2022]
Abstract
Thermophilic bacteria are of great value for industry and research communities. Unfortunately, the cellular processes and mechanisms of these organisms remain largely understudied. In the present study, we investigate how the inactivation of adenylate kinase (AK) affects the adenine nucleotide homeostasis of a gram-positive moderate thermophile, Geobacillus stearothermophilus strain NUB3621-R. AK plays a major role in the adenine nucleotide homeostasis of living cells and has been shown to be essential for the gram-negative mesophile Escherichia coli. To study the role of AK in the maintenance of adenylate energy charge (EC) and cell viability of G. stearothermophilus, we generated a recombinant strain of this organism in which its endogenous gene coding for the essential protein adenylate kinase (AK) has been replaced with the adk gene from the mesophile Bacillus subtilis. PCR, DNA sequencing and Southern analysis were performed to confirm proper gene replacement and preservation of neighboring genes. The highest growing temperature for recombinant cells was almost 20 degrees C lower than for wild-type cells (56 vs. 75 degrees C). This temperature-sensitive phenotype was secondary to heat inactivation of B. subtilis AK, as evidenced by enzyme activity assays and EC measurements. At higher temperatures (65 degrees C), recombinant cells also had lower EC values (0.09) compared to wild-type cells (0.45), which reflects a disruption of adenine nucleotide homeostasis following AK inactivation.
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Affiliation(s)
- Rafael Couñago
- Biochemistry and Cell Biology Department, Rice University, 6100 Main st. MS 140, Houston, TX 77251-1892, USA
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16
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Ravera S, Repaci E, Morelli A, Pepe IM, Botter R, Beruto D. Electromagnetic field of extremely low frequency decreased adenylate kinase activity in retinal rod outer segment membranes. Bioelectrochemistry 2004; 63:317-20. [PMID: 15110295 DOI: 10.1016/j.bioelechem.2003.10.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2003] [Revised: 09/19/2003] [Accepted: 10/06/2003] [Indexed: 10/26/2022]
Abstract
Adenylate kinase activity in rod outer segment membranes of bovine retina decreased of about 55% when exposed to an extremely low frequency electromagnetic field of 75 Hz and 250 microT. The effect was independent of the time of permanence in the field. Negligible effects of the field were found on the enzymatic activity of a soluble isoform of adenylate kinase or of rod outer segment membranes solubilized with Triton, suggesting the importance of the membrane in determining the conditions of the enzyme inactivation.
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Affiliation(s)
- S Ravera
- Department of DIBISAA, University of Genoa, Genoa, Italy
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17
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Sirikantaramas S, Morimoto S, Shoyama Y, Ishikawa Y, Wada Y, Shoyama Y, Taura F. The gene controlling marijuana psychoactivity: molecular cloning and heterologous expression of Delta1-tetrahydrocannabinolic acid synthase from Cannabis sativa L. J Biol Chem 2004; 279:39767-74. [PMID: 15190053 DOI: 10.1074/jbc.m403693200] [Citation(s) in RCA: 174] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Delta(1)-tetrahydrocannabinolic acid (THCA) synthase is the enzyme that catalyzes oxidative cyclization of cannabigerolic acid into THCA, the precursor of Delta(1)-tetrahydrocannabinol. We cloned a novel cDNA (GenBank trade mark accession number AB057805) encoding THCA synthase by reverse transcription and polymerase chain reactions from rapidly expanding leaves of Cannabis sativa. This gene consists of a 1635-nucleotide open reading frame, encoding a 545-amino acid polypeptide of which the first 28 amino acid residues constitute the signal peptide. The predicted molecular weight of the 517-amino acid mature polypeptide is 58,597 Da. Interestingly, the deduced amino acid sequence exhibited high homology to berberine bridge enzyme from Eschscholtzia californica, which is involved in alkaloid biosynthesis. The liquid culture of transgenic tobacco hairy roots harboring the cDNA produced THCA upon feeding of cannabigerolic acid, demonstrating unequivocally that this gene encodes an active THCA synthase. Overexpression of the recombinant THCA synthase was achieved using a baculovirus-insect expression system. The purified recombinant enzyme contained covalently attached FAD cofactor at a molar ratio of FAD to protein of 1:1. The mutant enzyme constructed by changing His-114 of the wild-type enzyme to Ala-114 exhibited neither absorption characteristics of flavoproteins nor THCA synthase activity. Thus, we concluded that the FAD binding residue is His-114 and that the THCA synthase reaction is FAD-dependent. This is the first report on molecular characterization of an enzyme specific to cannabinoid biosynthesis.
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18
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Munier-Lehmann H, Chenal-Francisque V, Ionescu M, Chrisova P, Foulon J, Carniel E, Bârzu O. Relationship between bacterial virulence and nucleotide metabolism: a mutation in the adenylate kinase gene renders Yersinia pestis avirulent. Biochem J 2003; 373:515-22. [PMID: 12879903 PMCID: PMC1223521 DOI: 10.1042/bj20030284] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nucleoside monophosphate kinases (NMPKs) are essential catalysts for bacterial growth and multiplication. These enzymes display high primary sequence identities among members of the family Enterobacteriaceae. Yersinia pestis, the causative agent of plague, belongs to this family. However, it was previously shown that its thymidylate kinase (TMPKyp) exhibits biochemical properties significantly different from those of its Escherichia coli counterpart [Chenal-Francisque, Tourneux, Carniel, Christova, Li de la Sierra, Barzu and Gilles (1999) Eur. J. Biochem. 265, 112-119]. In this work, the adenylate kinase (AK) of Y. pestis (AKyp) was characterized. As with TMPKyp, AKyp displayed a lower thermodynamic stability than other studied AKs. Two mutations in AK (Ser129Phe and Pro87Ser), previously shown to induce a thermosensitive growth defect in E. coli, were introduced into AKyp. The recombinant variants had a lower stability than wild-type AKyp and a higher susceptibility to proteolytic digestion. When the Pro87Ser substitution was introduced into the chromosomal adk gene of Y. pestis, growth of the mutant strain was altered at the non-permissive temperature of 37 degree C. In virulence testings, less than 50 colony forming units (CFU) of wild-type Y. pestis killed 100% of the mice upon subcutaneous infection, whereas bacterial loads as high as 1.5 x 10(4) CFU of the adk mutant were unable to kill any animals.
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Affiliation(s)
- Hélène Munier-Lehmann
- Laboatoire de Chimie Structurale des Macromolécules, Institut Pasteur, Cedex 15, France.
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19
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Zikmanis P, Kruce R, Auzina L. Interrelationships between Growth Yield, ATPase and Adenylate Kinase Activities inZymomonas mobilis. ACTA ACUST UNITED AC 2001. [DOI: 10.1002/1521-3846(200105)21:2<171::aid-abio171>3.0.co;2-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Miura K, Inouye S, Sakai K, Takaoka H, Kishi F, Tabuchi M, Tanaka T, Matsumoto H, Shirai M, Nakazawa T, Nakazawa A. Cloning and characterization of adenylate kinase from Chlamydia pneumoniae. J Biol Chem 2001; 276:13490-8. [PMID: 11278507 DOI: 10.1074/jbc.m009461200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chlamydiae proliferate only within the infected host cells and are thought to be "energy parasites," because they take up ATP from the host cell as an energy source. In the present study, we isolated from Chlamydia pneumoniae the gene encoding adenylate kinase (AK). Using the enzyme produced in Escherichia coli, its properties were characterized. K(m) values for AMP and for ADP of the purified C. pneumoniae AK (AKcpn) were each 330 microm, which is significantly higher than the reported values of other AKs, whereas K(m) for ATP was 24 microm, which was rather lower than others. AKcpn contains 1 g atom of zinc/mol of 24,000-dalton protein. Mass spectrometric analysis of AKcpn and analysis of properties of mutated AKcpn strongly suggested that zinc is associated with four cysteine residues in the LID domain of the enzyme. The apo-AKcpn that lost zinc retained AK activity, although K(m) for AMP of apo-AKcpn increased about 2-fold and V(max) decreased about one-half from that of holo-AKcpn. The apo-AKcpn was more thermolabile and sensitive to trypsin digestion than the holo-AKcpn. Moreover, the recovery in vitro of the AK activity during the renaturation process of the denatured apo-AKcpn was dependent on zinc. A mutated protein in which cysteine residues in the LID domain were substituted by other amino acids lost both zinc and enzyme activity. The mutated protein was more sensitive to protease than the apo-AKcpn. These results indicate that zinc in AKcpn, although not essential for the catalysis, stabilizes the enzyme and probably plays a crucial role in proper folding of the protein. Furthermore, the catalytic properties of AKcpn suggest a distinctive regulatory mechanism in the metabolism compared with AKs in other organisms.
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Affiliation(s)
- K Miura
- Department of Biochemistry, Central Laboratory for Biomedical Research and Education, Yamaguchi University School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan.
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21
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Notari L, Pepe IM, Cugnoli C, Morelli A. Adenylate kinase activity in rod outer segments of bovine retina. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1504:438-43. [PMID: 11245807 DOI: 10.1016/s0005-2728(01)00160-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The rod outer segments of bovine retina contain two different adenylate kinases: a soluble activity, which is not sensitive to calcium ion, and an activity bound to disk membranes, which is dependent on the calcium levels. In fact, the maximal activity associated to the disks is reached at Ca(2+) concentrations between 10(-6) and 10(-7) M, which is the range of calcium level actually present in the rod cell. The Michaelis-Menten kinetics of the enzyme activity on disk membranes was determined and the actual concentrations of ATP, AMP and ADP were measured in the photoreceptor outer segment. Therefore, the physiological relevance of the adenylate kinase activity was discussed considering the above results. The formation of ATP catalyzed by the enzyme seems appropriate to supply at least some of the reactions necessary for phototransduction, indicating that ATP could be regenerated from ADP directly on the disk membranes where the photoreception events take place.
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Affiliation(s)
- L Notari
- Institute of Biochemistry, University of Genoa, Italy
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22
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Burlacu-Miron S, Gilles AM, Popescu A, Bârzu O, Craescu CT. Multinuclear magnetic resonance studies of Escherichia coli adenylate kinase in free and bound forms. Resonance assignment, secondary structure and ligand binding. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 264:765-74. [PMID: 10491122 DOI: 10.1046/j.1432-1327.1999.00633.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The crystal structure of Escherichia coli adenylate kinase (AKe) revealed three main components: a CORE domain, composed of a five-stranded parallel beta-sheet surrounded by alpha-helices, and two peripheral domains involved in covering the ATP in the active site (LID) and binding of the AMP (NMPbind). We initiated a long-term NMR study aiming to characterize the solution structure, binding mechanism and internal dynamics of the various domains. Using single (15N) and double-labeled (13C and 15N) samples and double- and triple-resonance NMR experiments we assigned 97% of the 1H, 13C and 15N backbone resonances, and proton and 13Cbeta resonances for more than 40% of the side chains in the free protein. Analysis of a 15N-labeled enzyme in complex with the bi-substrate analogue [P1,P5-bis(5'-adenosine)-pentaphosphate] (Ap5A) resulted in the assignment of 90% of the backbone 1H and 15N resonances and 42% of the side chain resonances. Based on short-range NOEs and 1H and 13C secondary chemical shifts, we identified the elements of secondary structure and the topology of the beta-strands in the unliganded form. The alpha-helices and the beta-strands of the parallel beta-sheet in solution have the same limits (+/- 1 residue) as those observed in the crystal. The first helix (alpha1) appears to have a frayed N-terminal side. Significant differences relative to the crystal were noticed in the LID domain, which in solution exhibits four antiparallel beta-strands. The secondary structure of the nucleoside-bound form, as deduced from intramolecular NOEs and the 1Halpha chemical shifts, is similar to that of the free enzyme. The largest chemical shift differences allowed us to map the regions of protein-ligand contacts. 1H/2H exchange experiments performed on free and Ap5A-bound enzymes showed a general decrease of the structural flexibility in the complex which is accompanied by a local increased flexibility on the N-side of the parallel beta-sheet.
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23
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Munier-Lehmann H, Burlacu-Miron S, Craescu CT, Mantsch HH, Schultz CP. A new subfamily of short bacterial adenylate kinases with theMycobacteriumtuberculosis enzyme as a model: A predictive and experimental study. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19990801)36:2<238::aid-prot9>3.0.co;2-k] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Tourneux L, Bucurenci N, Lascu I, Sakamoto H, Briand G, Gilles AM. Substitution of an alanine residue for glycine 146 in TMP kinase from Escherichia coli is responsible for bacterial hypersensitivity to bromodeoxyuridine. J Bacteriol 1998; 180:4291-3. [PMID: 9696781 PMCID: PMC107429 DOI: 10.1128/jb.180.16.4291-4293.1998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The wild-type TMP kinases from Escherichia coli and from a strain hypersensitive to 5-bromo-2'-deoxyuridine were characterized comparatively. The mutation at codon 146 causes the substitution of an alanine residue for glycine in the enzyme, which is accompanied by changes in the relative affinities for 5-Br-UMP and TMP compared to those of the wild-type TMP kinase. Plasmids carrying the wild-type tmk gene from Escherichia coli or Bacillus subtilis, but not the defective tmk gene, restored the resistance to bromodeoxyuridine of an E. coli mutant strain.
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Affiliation(s)
- L Tourneux
- Laboratoire de Chimie Structurale des Macromolécules, Institut Pasteur, 75724 Paris Cedex 15, France
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25
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Perrier V, Burlacu-Miron S, Bourgeois S, Surewicz WK, Gilles AM. Genetically engineered zinc-chelating adenylate kinase from Escherichia coli with enhanced thermal stability. J Biol Chem 1998; 273:19097-101. [PMID: 9668094 DOI: 10.1074/jbc.273.30.19097] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In contrast with adenylate kinase from Gram-negative bacteria, the enzyme from Gram-positive organisms harbors a structural Zn2+ bound to 3 or 4 Cys residues in the structural motif Cys-X2-Cys-X16-Cys-X2-Cys/Asp. Site-directed mutagenesis of His126, Ser129, Asp146, and Thr149 (corresponding to Cys130, Cys133, Cys150, and Cys153 in adenylate kinase from Bacillus stearothermophilus) in Escherichia coli adenylate kinase was undertaken for determining whether the presence of Cys residues is the only prerequisite to bind zinc or (possible) other cations. A number of variants of adenylate kinase from E. coli, containing 1-4 Cys residues were obtained, purified, and analyzed for metal content, structural integrity, activity, and thermodynamic stability. All mutants bearing 3 or 4 cysteine residues acquired zinc binding properties. Moreover, the quadruple mutant exhibited a remarkably high thermal stability as compared with the wild-type form with preservation of the kinetic parameters of the parent enzyme.
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Affiliation(s)
- V Perrier
- Laboratoire de Chimie Structurale des Macromolécules, Institut Pasteur, 75724 Paris Cedex 15, France
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26
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Schultz CP, Ylisastigui-Pons L, Serina L, Sakamoto H, Mantsch HH, Neuhard J, Bârzu O, Gilles AM. Structural and catalytic properties of CMP kinase from Bacillus subtilis: a comparative analysis with the homologous enzyme from Escherichia coli. Arch Biochem Biophys 1997; 340:144-53. [PMID: 9126287 DOI: 10.1006/abbi.1997.9888] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
CMP kinases from Bacillus subtilis and from Escherichia coli are encoded by the cmk gene (formerly known as jofC in B. subtilis and as mssA in E. coli). Similar in their primary structure (43% identity and 67% similarity in amino acid sequence), the two proteins exhibit significant differences in nucleotide binding and catalysis. ATP, dATP, and GTP are equally effective as phosphate donors with E. coli CMP kinase whereas GTP is a poor substrate with B. subtilis CMP kinase. While CMP and dCMP are the best phosphate acceptors of both CMP kinases, the specific activity with these substrates and ATP as donor are 7- to 10-fold higher in the E. coli enzyme; the relative Vm values with UMP and CMP are 0.1 for the B. subtilis CMP kinase and 0.01 for the E. coli enzyme. CMP increased the affinity of E. coli CMP kinase for ATP or for the fluorescent analog 3'-anthraniloyl dATP by one order of magnitude but had no effect on the B. subtilis enzyme. The differences in the catalytic properties of B. subtilis and E. coli CMP kinases might be reflected in the structure of the two proteins as inferred from infrared spectroscopy. Whereas the spectrum of B. subtilis CMP kinase is dominated by a band at 1633 cm-1 (representing beta type structures), the spectrum of the E. coli enzyme is dominated by two bands at 1653 and 1642 cm-1 associated with alpha-helical and unordered structures, respectively. CMP induced similar spectral changes in both proteins with a rearrangement of some of the beta-structures. ATP increases the denaturation temperature of B. subtilis CMP kinase by 9.3 degrees C, whereas in the case of the E. coli enzyme, binding of ATP has only a minor effect.
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Affiliation(s)
- C P Schultz
- Institute for Biodiagnostics, National Research Council Canada, Winnipeg, Manitoba, Canada
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27
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Briand G, Perrier V, Kouach M, Takahashi M, Gilles AM, Bârzu O. Characterization of metal and nucleotide liganded forms of adenylate kinase by electrospray ionization mass spectrometry. Arch Biochem Biophys 1997; 339:291-7. [PMID: 9056261 DOI: 10.1006/abbi.1997.9877] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Complexes of adenylate kinase from Escherichia coli, Bacillus subtilis, and Bacillus stearothermophilus with the bisubstrate nucleotide analog P1,P5-di(adenosine 5')-pentaphosphate and with metal ions (Zn2+ and/or Mg2+) were analyzed by electrospray ionization mass spectrometry. P1,P5-di(adenosine 5')-pentaphosphate. adenylate kinase complex was detected in the positive mode at pH as low as 3.8. Binding of nucleotide to adenylate kinase stabilizes the overall structure of the protein and preserves the Zn2+ chelated form of the enzyme from the gram-positive organisms. In this way, it is possible in a single mass spectrometry experiment to screen metal-chelating adenylate kinases, without use of radioactively labeled compounds. Binding of Mg2+ to enzyme via P1,P5-di(adenosine 5')-pentaphosphate was also demonstrated by mass spectrometry. Although no amino acid side chain in adenylate kinase is supposed to interact with Mg2+, Asp93 in porcine muscle cytosolic enzyme, equivalent to Asp84 in the E. coli adenylate kinase, was proposed to stabilize the nucleotide.Mg2+ complex via water molecules.
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Affiliation(s)
- G Briand
- Laboratoire d'Application de Spectrométrie de Masse, Université de Lille II, Lille Cedex, 59045, France
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28
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Bucurenci N, Sakamoto H, Briozzo P, Palibroda N, Serina L, Sarfati RS, Labesse G, Briand G, Danchin A, Bărzu O, Gilles AM. CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases. J Biol Chem 1996; 271:2856-62. [PMID: 8576266 DOI: 10.1074/jbc.271.5.2856] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
CMP kinase from Escherichia coli is a monomeric protein of 225 amino acid residues. The protein exhibits little overall sequence similarities with other known NMP kinases. However, residues involved in binding of substrates and/or in catalysis were found conserved, and sequence comparison suggested conservation of the global fold found in adenylate kinases or in several CMP/UMP kinases. The enzyme was purified to homogeneity, crystallized, and analyzed for its structural and catalytic properties. The crystals belong to the hexagonal space group P6(3), have unit cell parameters a = b = 82.3 A and c = 60.7 A, and diffract x-rays to a 1.9 A resolution. The bacterial enzyme exhibits a fluorescence emission spectrum with maximum at 328 nm upon excitation at 295 nm, which suggests that the single tryptophan residue (Trp30) is located in a hydrophobic environment. Substrate specificity studies showed that CMP kinase from E. coli is active with ATP, dATP, or GTP as donors and with CMP, dCMP, and arabinofuranosyl-CMP as acceptors. This is in contrast with CMP/UMP kinase from Dictyostelium discoideum, an enzyme active on CMP or UMP but much less active on the corresponding deoxynucleotides. Binding of CMP enhanced the affinity of E. coli CMP kinase for ATP or ADP, a particularity never described in this family of proteins that might explain inhibition of enzyme activity by excess of nucleoside monophosphate.
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Affiliation(s)
- N Bucurenci
- Unité de Biochimie des Régulations Cellulaires, Institut Pasteur, Paris, France
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29
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Hemmer W, Furter-Graves EM, Frank G, Wallimann T, Furter R. Autophosphorylation of creatine kinase: characterization and identification of a specifically phosphorylated peptide. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1251:81-90. [PMID: 7669815 DOI: 10.1016/0167-4838(95)00083-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report that several different chicken and rabbit creatine kinase (CK)1 isoenzymes showed an incorporation of 32P when incubated with [gamma-32P]ATP in an autophosphorylation assay. This modification was was shown to be of covalent nature and resulted from an intramolecular phosphorylation reaction that was not dependent on the CK enzymatic activity. By limited proteolysis and sequence analysis of the resulting peptides, the autophosphorylation sites of chicken brain-type CK could be localized within the primary sequence of the enzyme to a 4.5 kDa peptide, spanning a region that is very likely an essential part of the active site of creatine kinase. Homologous peptides were found to be autophosphorylated in chicken muscle-type CK and a mitochondrial CK isoform. Phosphopeptide as well as mutant enzyme analysis provided evidence that threonine-282(2), threonine-289 and serine-285 are involved in the autophosphorylation of CK. Thr-282 and Ser-285 are located close to the reactive cysteine-283. Thr-289 is located within a conserved glycine-rich region highly homologous to the glycine-rich loop of protein kinases, which is known to be important for ATP binding. Thus, it seems likely that the described region constitutes an essential part of the active site of CK.
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Affiliation(s)
- W Hemmer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0654, USA
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30
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Perrier V, Surewicz WK, Glaser P, Martineau L, Craescu CT, Fabian H, Mantsch HH, Bârzu O, Gilles AM. Zinc chelation and structural stability of adenylate kinase from Bacillus subtilis. Biochemistry 1994; 33:9960-7. [PMID: 8061005 DOI: 10.1021/bi00199a019] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Adenylate kinase from Bacillus subtilis, like the enzyme from Bacillus stearothermophilus, contains a structural zinc atom. Cys153 in the enzyme from B. stearothermophilus, which is involved in the zinc coordination, is replaced in the adenylate kinase from B. subtilis by an aspartic acid residue. Therefore, we were interested in establishing whether this difference has an impact on the structure, the metal chelation, and the overall stability of these proteins. We also were interested in determining whether His138, which is conserved in many adenylate kinases, can act as a fourth partner in the metal chelation and, in general, whether His can successfully replace Cys or Asp in coordinating zinc in the adenylate kinase from B. subtilis. The adk gene from B. subtilis was cloned by polymerase chain reaction. The wild-type protein, together with several variants obtained by site-directed mutagenesis, were expressed in Escherichia coli and analyzed by biochemical and physicochemical methods. The H138N and D153C mutants of adenylate kinase from B. subtilis exhibited properties similar to those of the wild-type protein, indicating that His138 is not involved in metal coordination and that Asp153, just like Cys in the analogous position in the enzyme from B. stearothermophilus, can participate in zinc chelation. This is the first experimental evidence indicating that aspartic acid can be involved in the coordination of a structural zinc atom. On the other hand, the D153H and D153T variants showed significant changes in their zinc-binding properties. Dialysis of the latter proteins against buffer (in both the presence and the absence of 2 mM EDTA) resulted in removal of the metal ion and loss of enzymatic activity.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- V Perrier
- Unité de Biochimie des Régulations Cellulaires, Institut Pasteur, Paris, France
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31
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Gilles AM, Glaser P, Perrier V, Meier A, Longin R, Sebald M, Maignan L, Pistotnik E, Bârzu O. Zinc, a structural component of adenylate kinases from gram-positive bacteria. J Bacteriol 1994; 176:520-3. [PMID: 8288548 PMCID: PMC205078 DOI: 10.1128/jb.176.2.520-523.1994] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The recent finding that Bacillus stearothermophilus adenylate kinase contains a zinc atom coordinated to four cysteines prompted us to investigate the metal-binding properties of the enzyme from various bacteria. We conclude that zinc was present only in adenylate kinase from gram-positive species and that this property is correlated with the presence of three or four Cys residues in the sequence Cys-X2-Cys-X16-Cys-X2-Cys/Asp, in which X stands for different amino acid residues.
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Affiliation(s)
- A M Gilles
- Unité de Biochimie des Régulations Cellulaires, Institut Pasteur, Paris, France
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32
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Gilles AM, Sismeiro O, Munier H, Fabian H, Mantsch HH, Surewicz WK, Craescu CC, Barzu O, Danchin A. Structural and physico-chemical characteristics of Bordetella pertussis adenylate kinase, a tryptophan-containing enzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 218:921-7. [PMID: 8281944 DOI: 10.1111/j.1432-1033.1993.tb18448.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The adk gene from the Gram-negative pathogen Bordetella pertussis was cloned by complementing the thermosensitive Escherichia coli adk strain CR341T28. B. pertussis adenylate kinase is a 218-amino-acid protein that has high similarity with adenylate kinase from Escherichia coli and Hemophilus influenzae (57%). A distinct characteristic of enzyme from B. pertussis, not found in other bacterial adenylate kinases, is the presence of a tryptophan residue at position 185. Although distant from the catalytic site, this single tryptophan serves as a convenient probe for monitoring the binding of nucleotide substrates or analogs to the enzyme. Differential scanning calorimetry and equilibrium unfolding experiments in guanidine.HCl indicate similar stabilities for adenylate kinase from B. pertussis and E. coli. An extensive comparison between physico-chemical properties of adenylate kinase from B. pertussis and the enzyme from E. coli showed that the kinetic and structural properties of the two enzymes are very similar. However, infrared spectroscopy has allowed to identify small but significant differences in the secondary structure of the two proteins.
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Affiliation(s)
- A M Gilles
- Unitë de Biochimie des Régulations Cellulaires, Institut Pasteur, Paris, France
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33
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Deppert WR, Normann J, Wagner E. Adenylate kinase from plant tissues. Influence of ribonuclease on binding properties on Mono Q. J Chromatogr A 1992; 625:13-9. [PMID: 12126104 DOI: 10.1016/0021-9673(92)87216-u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Adenylate kinases modulate the three adenine nucleotide pools and were found to be localized as isoenzymes in different tissues and organelles in animals and plants. For investigations of adenylate kinase isoenzymes from plant tissues different plant extracts were examined by anion-exchange chromatography. During investigations with the strong anion exchanger Mono Q, adenylate kinase activity eluted in the void volume. This void volume activity did not always occur, but depended on the age of the plants and light treatment. The nature of the factors affecting void volume activity could only be partially resolved. It could be shown that RNase treatment at the beginning of extraction led to the disappearance of void volume activity, whereas an untreated extract still showed this activity.
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Affiliation(s)
- W R Deppert
- Institut für Biologie II, Universität Freiburg, Germany
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34
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Structural and functional consequences of amino acid substitutions in the second conserved loop of Escherichia coli adenylate kinase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54334-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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35
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Identification of valine/leucine/isoleucine and threonine/alanine/glycine proton-spin systems of Escherichia coli adenylate kinase by selective deuteration and selective protonation. Biochem J 1991; 273(Pt 2):311-6. [PMID: 1991031 PMCID: PMC1150215 DOI: 10.1042/bj2730311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Adenylate kinase from two types of Escherichia coli strains, a wild-type and a leucine-auxotrophic strain, was purified. On the one hand, growing the leucine-auxotrophic bacteria on a medium containing deuterated leucine yielded E. coli adenylate kinase with all leucine residues deuterated. On the other hand, by growing the wild-type bacteria on deuterated medium with phenylalanine, threonine and isoleucine present as protonated specimens, 80% randomly deuterated enzyme with protonated phenylalanine, threonine and isoleucine residues could be prepared. Use of these proteins enabled identification of the spin systems of these amino acid residues in the n.m.r. spectra of the protein.
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36
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Liang P, Phillips GN, Glaser M. Assignment of the nucleotide binding sites and the mechanism of substrate inhibition of Escherichia coli adenylate kinase. Proteins 1991; 9:28-36. [PMID: 2017434 DOI: 10.1002/prot.340090105] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Site-directed mutagenesis of key amino acids of adenylate kinase has been used to suggest a new model for the location of the AMP and ATP binding sites. Phe-86 and Tyr-133, which are in close contact with the inhibitor Ap5A according to previous crystallographic results, have been independently changed to tryptophan and other amino acids. The Phe-86----Trp mutant had a 3- to 6-fold change in the Km for ATP and a 44-fold increase in the Km for AMP with a simultaneous loss of AMP substrate inhibition. Thus Phe-86 is probably in close contact with bound AMP. The Tyr-133----Trp mutant showed no large effects on enzyme kinetics and suggests that the previous assignment of Ap5A occupying natural adenosine binding sites is probably incorrect. A temperature-sensitive Leu-107----Gln mutant showed a 6-fold decrease in the Km for ATP and no effect on AMP binding, suggesting that this amino acid is near the ATP binding site. Changes in the fluorescence of single tryptophan-containing mutant enzymes provided specific information about AMP and ATP binding. The fluorescence results are consistent with the kinetic studies, and also suggest that AMP substrate inhibition is caused by the formation of an abortive complex that prevents the release of product.
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Affiliation(s)
- P Liang
- Department of Biochemistry, University of Illinois, Urbana 61801
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37
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Wiesmüller L, Noegel AA, Bârzu O, Gerisch G, Schleicher M. cDNA-derived sequence of UMP-CMP kinase from Dictyostelium discoideum and expression of the enzyme in Escherichia coli. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39331-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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38
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Bârzu T, Lormeau JC, Petitou M, Michelson S, Choay J. Heparin-derived oligosaccharides: affinity for acidic fibroblast growth factor and effect on its growth-promoting activity for human endothelial cells. J Cell Physiol 1989; 140:538-48. [PMID: 2550475 DOI: 10.1002/jcp.1041400320] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The minimal structural requirements for the interaction of heparin with acidic fibroblast growth factor (aFGF) were investigated. Oligosaccharides (tetra- to decasaccharides) obtained by nitrous acid depolymerisation of standard heparin were separated by affinity chromatography on Sepharose-immobilised aFGF. The shortest fragment retained by the affinity column at 0.2 M NaCl and eluted at 1 M NaCl was a "regular" hexasaccharide, a trimer of the most abundant disaccharide sequence in heparin. More complex octa- and decasaccharides were also retained by the column. The oligosaccharides eluted by 1 M NaCl from the affinity column ("high-affinity" oligosaccharides) and those washed from the column at 0.2 M NaCl ("low-affinity" oligosaccharides) were compared for their capacity to protect aFGF from proteolysis and to potentiate its mitogenic activity. At a low ionic strength, all oligosaccharides tested, except the "regular" disaccharide, protected aFGF against trypsin and collagenase digestion. At higher ionic strength (greater than 0.2 M NaCl), only high-affinity oligosaccharides showed a protective effect. The high-affinity oligosaccharides (hexa- to decasaccharides) potentiated the mitogenic activity of aFGF, as measured by [3H]thymidine incorporation into DNA of human fibroblasts. The effect of the oligosaccharides on human endothelial cell proliferation was more complex: inhibition of proliferation was observed in the presence of serum and low concentrations of aFGF (1-5 ng/ml) and potentiation in the presence of higher concentrations of aFGF. The potentiating effect increased as a function of molecular size of the heparin fragments and, for a given size, as a function of the anionic charge of the oligosaccharide. Our results suggest that inhibition of cell proliferation by heparin may result from interference with an autocrine basic FGF-like activity.
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Haase GH, Brune M, Reinstein J, Pai EF, Pingoud A, Wittinghofer A. Adenylate kinases from thermosensitive Escherichia coli strains. J Mol Biol 1989; 207:151-62. [PMID: 2544733 DOI: 10.1016/0022-2836(89)90446-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The adk genes from several thermosensitive (ts) mutants of Escherichia coli were cloned and sequenced. The mutations responsible for the thermolability of the gene product, the enzyme adenylate kinase, were established. From five independently isolated strains analysed, two contain a CCG to TCG transition changing proline 87 to serine (P87S), another two have a TCT to TTT transition that mutates serine 129 to phenylalanine (S129F), and the last one was found not to contain a mutation in the adk gene. Overproducing strains were constructed that contain ts genes in the genome as well as in the plasmids. These strains grow at high temperature, although much slower than wild-type. Most probably, the high rate of synthesis of adenylate kinase compensates for the destruction of the thermolabile protein by the elevated temperature. Mutated proteins were purified. The P87S but not the S129F mutation was found to cause thermosensitivity of the adenylate kinase reaction. Revertants of thermosensitivity were isolated and the nature of the mutation was determined by the RNase digestion method of RNA-DNA hybrids and by DNA sequencing. The revertants of the P87S mutation regained the wild-type sequence, whereas the revertants of the S129F strain retained the original mutation in the adenylate kinase gene. These results are discussed in the light of the three-dimensional structure of the enzyme and the possible role of adenylate kinase in phospholipid synthesis.
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Affiliation(s)
- G H Haase
- Abteilung Biophysik, Max-Planck-Institut für Medizinische Forschung, Heidelberg, FRG
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40
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Reinstein J, Gilles AM, Rose T, Wittinghofer A, Saint Girons I, Bârzu O, Surewicz WK, Mantsch HH. Structural and catalytic role of arginine 88 in Escherichia coli adenylate kinase as evidenced by chemical modification and site-directed mutagenesis. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83156-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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41
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Klaus W, Scharf M, Zimmermann S, Rösch P. Two-dimensional NMR studies of the porcine muscle adenylate kinase. Biochemistry 1988; 27:5407-11. [PMID: 2846035 DOI: 10.1021/bi00415a004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Porcine adenylate kinase was subjected to one- and two-dimensional proton NMR studies in order to identify amino acid spin systems and obtain sequence-specific resonance assignments. With a combination of results from a map of side-chain distances resulting from the refined X-ray crystallographic data and nuclear Overhauser effect spectroscopy (NOESY), assignments are suggested for all the aromatic spin systems.
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Affiliation(s)
- W Klaus
- Max-Planck-Institute for Medical Research, Department of Biophysics, Heidelberg, FRG
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42
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Reinstein J, Brune M, Wittinghofer A. Mutations in the nucleotide binding loop of adenylate kinase of Escherichia coli. Biochemistry 1988; 27:4712-20. [PMID: 2844237 DOI: 10.1021/bi00413a020] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The adk gene of Escherichia coli has been used to overexpress the adenylate kinase protein in two ways: (1) by cloning the adk gene with its own promoter into pEMBL plasmids, which have an increased copy number, and (2) by deleting the adk promoter and cloning the gene behind the regulatable tac promoter. Adenylate kinase comprises up to 40% of the soluble cellular extracts from E. coli strains containing these plasmids. Mutations have been introduced into the gene by site-directed mutagenesis to exchange amino acids in the nucleotide binding loop, which is highly conserved in many mononucleotide binding proteins. The mutation of Lys13----Gln is nearly inactive, whereas the Pro9----Leu and the Gly10----Val mutant proteins have an increased Km for both substrates and a Vmax that is similar to wild type. Proton NMR measurements of the proteins show that a major structural change seems to have taken place for the Pro9----Leu and Gly10----Val mutants. The results are discussed in the light of the kinetic mechanism for adenylate kinase and the three-dimensional structure of the protein.
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Affiliation(s)
- J Reinstein
- Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Heidelberg, West Germany
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Gilles AM, Marlière P, Rose T, Sarfati R, Longin R, Meier A, Fermandjian S, Monnot M, Cohen GN, Bârzu O. Conservative replacement of methionine by norleucine in Escherichia coli adenylate kinase. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68463-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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44
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Bock I, Reinstein J, Brune M, Wittinghofer A, Rösch P. Proton-nuclear magnetic resonance studies of the aromatic spin systems of Escherichia coli adenylate kinase. J Mol Biol 1988; 200:745-8. [PMID: 2842509 DOI: 10.1016/0022-2836(88)90486-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Escherichia coli adenylate kinase has a very well resolved proton nuclear magnetic resonance spectrum in the region containing signals from aromatic amino acid side-chains. We found that the protein is structurally stable over a wide pH range and renatures spontaneously after acidic as well as basic denaturation. Only one out of the three histidyl imidazole rings titrates on changing the pH and has a pka value of 7.6. Two-dimensional nuclear magnetic resonance spectroscopy studies allowed use to identify most of the enzyme's aromatic spin systems, and by investigation of a mutant protein we were able to assign the aromatic part of the spin system of Tyr24 unambiguously.
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Affiliation(s)
- I Bock
- Max-Planck-Institute for Medical Research, Dept. of Biophysics, Heidelberg, Germany
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Althoff S, Zambrowicz B, Liang P, Glaser M, Phillips GN. Crystallization and preliminary X-ray analysis of Escherichia coli adenylate kinase. J Mol Biol 1988; 199:665-6. [PMID: 2832615 DOI: 10.1016/0022-2836(88)90310-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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46
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47
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48
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Nealon DA. Rapid purification of adenylate kinase from human erythrocytes and skeletal muscle. Arch Biochem Biophys 1986; 250:19-22. [PMID: 3021063 DOI: 10.1016/0003-9861(86)90696-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Adenylate kinase from human erythrocytes and skeletal muscle can be purified to homogeneity by a new procedure based on DEAE-Sepharose and Blue Sepharose affinity chromatography and Sephadex G-75 fractionation. For the enzyme purified from erythrocytes the specific activity is 3,000 U/mg of protein, and the overall yield is 70%. For the enzyme purified from skeletal muscle the specific activity is 2,075 U/mg of protein, and the overall yield is 44%. The sequence of steps takes advantage of the high isoelectric point, the high affinity for Blue Sepharose, and the low molecular weight of the isoenzyme from these two human tissues.
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Gilles AM, Saint-Girons I, Monnot M, Fermandjian S, Michelson S, Bârzu O. Substitution of a serine residue for proline-87 reduces catalytic activity and increases susceptibility to proteolysis of Escherichia coli adenylate kinase. Proc Natl Acad Sci U S A 1986; 83:5798-802. [PMID: 3016722 PMCID: PMC386382 DOI: 10.1073/pnas.83.16.5798] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Amino acid analysis, HPLC separation of trypsin digests, and sequence analysis showed that the thermosensitivity of the adenylate kinase (EC 2.7.4.3) from Escherichia coli K-12 strain CR341 T28 results from substitution of a serine residue for proline-87 in the wild-type enzyme. This mutation is accompanied by decreased affinity for nucleotide substrates and decreased catalysis. Circular dichroism spectroscopy showed a significant change of the secondary structure. This mainly corresponds to a reduction in alpha-helix content (39%) of mutant protein as compared to wild-type adenylate kinase (50%). Altered conformation of thermosensitive adenylate kinase was also manifested by an increase in susceptibility to proteolysis by trypsin. Ap5A and ATP, known to induce important conformational changes in eukaryotic adenylate kinase(s), protected the mutant enzyme against inactivation by trypsin. This seems to indicate that the "loosening" of the three-dimensional structure of E. coli adenylate kinase by proline----serine substitution is largely compensated for when an enzyme X ATP or enzyme X Ap5A complex is formed.
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50
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Rösch P, Gross KH. Assignment of aromatic spin systems in the 1H nuclear magnetic resonance spectrum of adenylate kinase. J Mol Biol 1985; 182:341-5. [PMID: 2987513 DOI: 10.1016/0022-2836(85)90350-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A combination of selective spin decoupling, two-dimensional double quantum spectroscopy, correlated spectroscopy (COSY), and pH titration experiments brought about the assignment of all tyrosyl spin systems and completed the assignment of the histidyl spin systems in porcine adenylate kinase. In the detection of the tyrosyl spin systems it proved to be advantageous to resort to the COSY method rather than to two-dimensional double quantum spectroscopy. In the titration experiments, His189 revealed a second apparent pK value at pH 8.3, which is explained by deprotonation of the adjacent residue Cys187. None of the seven tyrosyl side-chains shows any evidence for deprotonation up to the point of denaturation of the protein, which took place around pH 10.
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