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The characterization of novel monomeric creatine kinases in the early branching Alveolata species, Perkinsus marinus: Implications for phosphagen kinase evolution. Comp Biochem Physiol B Biochem Mol Biol 2022; 262:110758. [PMID: 35598705 DOI: 10.1016/j.cbpb.2022.110758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022]
Abstract
The genome of the unicellular molluscan parasite Perkinsus marinus contains at least five genes coding for putative creatine kinases (CK), a phosphoryl transfer enzyme which plays a key role in cellular energy transactions. Expression and kinetic analyses of three of the P. marinus CKs revealed them to be true CKs with catalytic properties in the range of typical metazoan CKs. A sequence comparison of the P. marinus CKs with a range of CK dimers and other dimeric phosphoryl transfer enzymes in this family (phosphagen kinases) showed that the P. marinus CKs lacked some of the critical residues involved in dimer stabilization, a trait all previously characterized CKs share. Size exclusion chromatography of all three expressed P. marinus CK constructs indicated they are monomeric, consistent with the observed lack of some critical dimer stabilizing residues. Phylogenetic analyses of the P. marinus CKs and putative dinoflagellate CKs with a broad range of monomeric and dimeric phosphagen kinases revealed that the Perkinsus CKs form a distinct, well-supported clade with dinoflagellate CKs which also lack the dimer stabilizing residues. Analysis of the genomic data for P. marinus showed the presence of putative genes for the two enzymes associated with creatine biosynthesis. CK in higher organisms plays a critical role in energy buffering in cell types displaying high and variable rates of ATP turnover. The presence of multiple CKs and the creatine biosynthetic pathway in P. marinus indicates that this unicellular parasite has the full complement of molecular machinery for CK-mediated energy buffering.
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Yang Z, Huang X, Liao H, Zhang Z, Sun F, Kou S, Bao Z. Structure and functional analysis reveal an important regulated role of arginine kinase in Patinopecten yessoensis under low pH stress. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 222:105452. [PMID: 32092594 DOI: 10.1016/j.aquatox.2020.105452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Arginine kinase (AK), an important member of the phosphokinase family, is involved in temporal and spatial adenosine triphosphate (ATP) buffering systems. AK plays an important role in physiological function and metabolic regulations, in particular tissues with high and fluctuating energy demands. In present study, four AK genes were firstly identified from Yesso scallop (Patinopecten yessoensis) genome, respectively named PyAK1-4. PyAKs have highly conserved structures with a six-exon/five-exon structure, except for PyAK3. PyAK3 contains an unusual two-domain structure and a "bridge intron" between the two domains, which may originate from gene duplication and subsequent fusion. Phylogenetic analysis showed that all PyAKs belonged to an AK supercluster together with other AK proteins from Mollusca, Platyhelminthes, Arthropoda, and Nematode. A transcriptome database demonstrated that PyAK3 and PyAK4 were the main functional executors with high expression level during larval development and in adult tissues, while PyAK1 and PyAK2 were expressed at a low level. Furthermore, both PyAK2 and PyAK3 showed notably high expression in the male gonad, and PyAK4 was broadly expressed in almost all tissues with the highest level in striated muscle, indicating a tissue-specific expression pattern of PyAKs. In addition, quantitative real-time PCR results demonstrated that the expression of PyAK2, PyAK3 and PyAK4 were significantly upregulated in response to pH stress, especially in an extremely acidifying condition (pH 6.5), revealing the possible involvement of PyAKs in energetic homeostasis during environmental changes. Collectively, a comprehensive analysis of PyAKs was conducted in P. yessoensis. The diversity of PyAKs and their specific expression patterns promote a better understanding of energy metabolism in the growth, development and environmental response of P. yessoensis.
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Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China
| | - Zhengrui Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Fanhua Sun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Sihua Kou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Matsuo T, Yano D, Uda K, Iwasaki N, Suzuki T. Arginine Kinases from the Precious Corals Corallium rubrum and Paracorallium japonicum: Presence of Two Distinct Arginine Kinase Gene Lineages in Cnidarians. Protein J 2017; 36:502-512. [PMID: 29022133 DOI: 10.1007/s10930-017-9745-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The cDNA sequence of arginine kinase (AK) from the precious coral Corallium rubrum was assembled from transcriptome sequence data, and the deduced amino acid sequence of 364 residues was shown to conserve the structural features characteristic of AK. Based on the amino acid sequence, the DNA coding C. rubrum AK was synthesized by overlap extension PCR to prepare the recombinant enzyme. The following kinetic parameters were determined for the C. rubrum enzyme: K aArg (0.10 mM), K iaArg (0.79 mM), K aATP (0.23 mM), K iaATP (2.16 mM), and k cat (74.3 s-1). These are comparable with the kinetic parameters of other AKs. However, phylogenetic analysis suggested that the C. rubrum AK sequence has a distinct origin from that of other known cnidarian AKs with unusual two-domain structure. Using oligomers designed from the sequence of C. rubrum AK, the coding region of genomic DNA of another coral Paracorallium japonicum AK was successfully amplified. Although the nucleotide sequences differed between the two AKs at 14 positions in the coding region, all involved synonymous substitutions, giving the identical amino acid sequence. The P. japonicum AK gene contained one intron at a unique position compared with other cnidarian AK genes. Together with the observations from phylogenetic analysis, the comparison of exon/intron organization supports the idea that two distinct AK gene lineages are present in cnidarians. The difference in the nucleotide sequence between the coding regions of C. rubrum and P. japonicum AKs was 1.28%, which is twice that (0.54%) of mitochondrial DNA, is consistent with the general observation that the mitochondrial genome evolves slower than the nuclear one in cnidarians.
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Affiliation(s)
- Tomoka Matsuo
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan
| | - Daichi Yano
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan
| | - Kouji Uda
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan
| | - Nozomu Iwasaki
- Faculty of Geo-Environment Science, Rissho University, Magechi 1700, Kumagaya, 360-0194, Japan
| | - Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan.
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Wickramasinghe S, Yatawara L, Nagataki M, Agatsuma T. Arginine kinase in Toxocara canis: Exon-intron organization, functional analysis of site-directed mutants and evaluation of putative enzyme inhibitors. ASIAN PAC J TROP MED 2016; 9:995-1001. [PMID: 27794395 DOI: 10.1016/j.apjtm.2016.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 06/15/2016] [Accepted: 07/15/2016] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES To determine exon/intron organization of the Toxocara canis (T. canis) AK (TCAK) and to test green and black tea and several other chemicals against the activity of recombinant TCAK in the guanidino-specific region by site-directed mutants. METHODS Amplification of genomic DNA fragments containing introns was carried out by PCRs. The open-reading frame (1200 bp) of TCAK (wild type) was cloned into the BamH1/SalI site of pMAL-c2X. The maltose-binding protein-TCAK fusion protein was expressed in Escherichia coli TB1 cells. The purity of the expressed enzyme was verified by SDS-PAGE. Mutations were introduced into the guanidino-specific region and other areas of pMAL/TCAK by PCR. Enzyme activity was measured with an NADH-linked assay at 25 °C for the forward reaction (phosphagen synthesis). RESULTS Arginine kinase in T. canis has a seven-exon/six-intron gene structure. The lengths of the introns ranged from 542 bp to 2 500 bp. All introns begin with gt and end with ag. Furthermore, we measured the enzyme activity of site-directed mutants of the recombinant TCAK. The Km value of the mutant (Alanine to Serine) decreased indicating a higher affinity for substrate arginine than the wild-type. The Km value of the mutant (Serine to Glycine) increased to 0.19 mM. The Km value (0.19 mM) of the double mutant (Alanine-Serine to Serine-Glycine) was slightly greater than in the wild-type (0.12 mM). In addition, several other chemicals were tested; including plant extract Azadiracta indica (A. indica), an aminoglycoside antibiotic (aminosidine), a citrus flavonoid glycoside (rutin) and a commercially available catechin mixture against TCAK. Green and black tea (1:10 dilution) produced 15% and 25% inhibition of TCAK, respectively. The extract of A. indica produced 5% inhibition of TCAK. Moreover, green and black tea produced a non-competitive type of inhibition and A. indica produced a mixed-type of inhibition on TCAK. CONCLUSIONS Arginine kinase in T. canis has a seven-exon/six-intron gene structure. However, further studies are needed to identify a specific compound within the extract causing the inhibitory effect and also to determine the molecular mechanisms behind inhibition of arginine kinase in T. canis.
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Affiliation(s)
- Susiji Wickramasinghe
- Department of Parasitology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka.
| | - Lalani Yatawara
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Mitsuru Nagataki
- Department of Environmental Health Sciences, Kochi Medical School, Oko, Nankoku City, Kochi Ken 783-8505, Japan
| | - Takeshi Agatsuma
- Department of Environmental Health Sciences, Kochi Medical School, Oko, Nankoku City, Kochi Ken 783-8505, Japan
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Tracing the structural evolution of eukaryotic ATP binding cassette transporter superfamily. Sci Rep 2015; 5:16724. [PMID: 26577702 PMCID: PMC4649718 DOI: 10.1038/srep16724] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/19/2015] [Indexed: 01/12/2023] Open
Abstract
The ATP binding cassette (ABC) transporters superfamily is one of the largest classes of membrane proteins. The core of the ABC transporter protein is composed of transmembrane domains (TMDs) and nucleotide binding domains (NBD). Eukaryotes ABC transporters are classified into seven main families (ABCA to ABCG) based on sequence similarity and domain organizations. With different domain number and domain organizations, eukaryote ABC transporters show diverse structures: the single structure (NBD or TMD), the ABC2 structure (NBD-NBD), the half structure (TMD-NBD or NBD-TMD) and the full structure (TMD-NBD-TMD-NBD or NBD-TMD-NBD-TMD). However, studies on how various ABC transporter gene structures evolved is still absent. Therefore, in this study, we comprehensively investigated the structural evolution of eukaryotic ABC transporters. The seven eukaryote ABC transporter families (A to G) fell into three groups: A&G group, B,C&D group and E&F group. There were at least four times the number of NBD and TMD fusion events in the origin of the half structure transporter. Two fusion modes were found in the full and ABC2 structure origination. Based on these findings, we present a putative structural evolutionary path of eukaryote ABC transporters that will increase our understanding on their origin, divergence and function.
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Okazaki N, Motomura S, Okazoe N, Yano D, Suzuki T. Cooperativity and evolution of Tetrahymena two-domain arginine kinase. Int J Biol Macromol 2015; 79:696-703. [PMID: 26049117 DOI: 10.1016/j.ijbiomac.2015.05.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/15/2015] [Accepted: 05/24/2015] [Indexed: 11/30/2022]
Abstract
Tetrahymena pyriformis contains two arginine kinases, a 40-kDa enzyme (AK1) with a myristoylation signal sequence at the N-terminus and a two-domain 80-kDa enzyme (AK2). The former is localized mainly in cilia and the latter is in the cytoplasm. AK1 was successfully synthesized using an insect cell-free protein synthesis system and subjected to peptide mass fingerprinting (PMF) analysis. The masses corresponding to unmodified N-terminal tryptic peptide or N-terminal myristoylated peptide were not observed, suggesting that N-terminal peptides were not ionized in this analysis. We performed PMF analyses for two other phosphagen kinases (PKs) with myristoylation signals, an AK from Nematostella vectensis and a PK from Ectocarpus siliculosus. In both cases, the myristoylated, N-terminal peptides were clearly identified. The differences between the experimental and theoretical masses were within 0.0165-0.0583 Da, supporting the accuracy of the identification. Domains 1 and 2 of Tetrahymena two-domain AK2 were expressed separately in Escherichia coli and the extent of cooperativity was estimated on the basis of their kinetic constants. The results suggested that each of the domains functions independently, namely no cooperativity is displayed between the two domains. This is in sharp contrast to the two-domain AK from Anthopleura.
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Affiliation(s)
- Noriko Okazaki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Shou Motomura
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Nanaka Okazoe
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Daichi Yano
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan.
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The Inhibitory Effects of Cu(2+) on Exopalaemon carinicauda Arginine Kinase via Inhibition Kinetics and Molecular Dynamics Simulations. Appl Biochem Biotechnol 2015; 176:1217-36. [PMID: 25935224 DOI: 10.1007/s12010-015-1641-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/21/2015] [Indexed: 12/28/2022]
Abstract
We studied the Cu(2+)-mediated inhibition and aggregation of Exopalaemon carinicauda arginine kinase (ECAK). We found that Cu(2+) significantly inactivated ECAK activity and double-reciprocal kinetics demonstrated that Cu(2+) induced noncompetitive inhibition of arginine and ATP (IC50 = 2.27 ± 0.16 μM; K i for arginine = 13.53 ± 3.76; K i for ATP = 4.02 ± 0.56). Spectrofluorometry results showed that Cu(2+) induced ECAK tertiary structural changes including the exposure of hydrophobic surfaces that directly induced ECAK aggregation. The addition of osmolytes such as glycine and proline successfully blocked ECAK aggregation induced by Cu(2+) and recovered ECAK activity. We built a 3D structure for ECAK using the ECAK ORF gene sequence. Molecular dynamics (MD) and docking simulations between ECAK and Cu(2+) were conducted to elucidate the binding mechanisms. The results showed that Cu(2+) blocked the entrance to the ATP active site; these results are consistent with the experimental result that Cu(2+) induced ECAK inactivation. Since arginine kinase (AK) plays an important role in cellular energy metabolism in invertebrates, our study can provide new information about the effect of Cu(2+) on ECAK enzymatic function and unfolding, including aggregation, and the protective effects of osmolytes on ECAK folding to better understand the role of the invertebrate ECAK metabolic enzyme in marine environments.
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Merceron R, Awama AM, Montserret R, Marcillat O, Gouet P. The substrate-free and -bound crystal structures of the duplicated taurocyamine kinase from the human parasite Schistosoma mansoni. J Biol Chem 2015; 290:12951-63. [PMID: 25837252 DOI: 10.1074/jbc.m114.628909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 01/01/2023] Open
Abstract
The taurocyamine kinase from the blood fluke Schistosoma mansoni (SmTK) belongs to the phosphagen kinase (PK) family and catalyzes the reversible Mg(2+)-dependent transfer of a phosphoryl group between ATP and taurocyamine. SmTK is derived from gene duplication, as are all known trematode TKs. Our crystallographic study of SmTK reveals the first atomic structure of both a TK and a PK with a bilobal structure. The two unliganded lobes present a canonical open conformation and interact via their respective C- and N-terminal domains at a helix-mediated interface. This spatial arrangement differs from that observed in true dimeric PKs, in which both N-terminal domains make contact. Our structures of SmTK complexed with taurocyamine or l-arginine compounds explain the mechanism by which an arginine residue of the phosphagen specificity loop is crucial for substrate specificity. An SmTK crystal was soaked with the dead end transition state analog (TSA) components taurocyamine-NO3 (2-)-MgADP. One SmTK monomer was observed with two bound TSAs and an asymmetric conformation, with the first lobe semiclosed and the second closed. However, isothermal titration calorimetry and enzyme kinetics experiments showed that the two lobes function independently. A small angle x-ray scattering model of SmTK-TSA in solution with two closed active sites was generated.
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Affiliation(s)
- Romain Merceron
- From the Institut de Biologie et Chimie des Protéines, BMSSI-IBCP, UMR 5086 CNRS Université Lyon 1, 7, Passage du Vercors, 69367 Lyon Cedex 07, France and
| | - Ayman M Awama
- the Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR 5246 CNRS Université Lyon 1, 69622 Villeurbanne, France
| | - Roland Montserret
- From the Institut de Biologie et Chimie des Protéines, BMSSI-IBCP, UMR 5086 CNRS Université Lyon 1, 7, Passage du Vercors, 69367 Lyon Cedex 07, France and
| | - Olivier Marcillat
- the Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR 5246 CNRS Université Lyon 1, 69622 Villeurbanne, France
| | - Patrice Gouet
- From the Institut de Biologie et Chimie des Protéines, BMSSI-IBCP, UMR 5086 CNRS Université Lyon 1, 7, Passage du Vercors, 69367 Lyon Cedex 07, France and
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Phosphagen kinase in Schistosoma japonicum: II. Determination of amino acid residues essential for substrate catalysis using site-directed mutagenesis. Mol Biochem Parasitol 2014; 194:56-63. [PMID: 24815317 DOI: 10.1016/j.molbiopara.2014.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 11/21/2022]
Abstract
Phosphagen kinases (PKs) play major roles in the regulation of energy metabolism in animals. Creatine kinase (CK) is the sole PK in vertebrates, whereas several PKs are present in invertebrates. We previously identified a contiguous dimer taurocyamine kinase (TK) from the trematode Schistosoma japonicum (Sj), a causative agent of schistosomiasis. SjTK contiguous dimer is comprised of domain 1 (D1) and domain 2 (D2). In this study, we used SjTK contiguous dimer (SjTKD1D2) or truncated single-domain constructs (SjTKD1 or SjTKD2) and employed site-directed mutagenesis to investigate the enzymatic properties of TK mutants. Mutation in SjTKD1 or SjTKD2 (D1E222G or D2E225G) caused complete loss of activity for the substrate taurocyamine. Likewise, a double mutant (D1E222GD2E225G) in the contiguous dimer (D1D2) exhibited complete loss of activity for the substrate taurocyamine. However, catalytic activity in the contiguous dimer remained in both of D1 inactive mutant (D1D2D1E222G) and D2 inactive mutant (D1D2D2E225G), suggesting that efficient catalysis of SjTKD1D2 is dependent on the activity of D1 and D2. The catalytic efficiency of the mixture of both single domains (WTD1+WTD2) showed same enzymatic properties (Km(Tauro)=0.68;Vmax/Km(Tauro)=137.04) to WTD1D2 (Km(Tauro)=0.47; Vmax/Km(Tauro)=144.30). This result suggests that the contiguous dimeric structure is not essential for the catalytic efficiencies of both domains of SjTK. Vmax/Km(Tauro) of the mixture of wild-type and inactivated domains (78.02 in WTD1+D2E225G and 128.24 in D1E222G+WTD2) were higher than the corresponding mutants (47.25 in D1D2D1E222G and 46.77 in D1D2D2E225G). To identify amino acid residues that are critical for taurocyamine binding, we performed alanine scanning mutagenesis at positions 57-63 on the guanidino specificity (GS) region of the SjTKD1, which is considered to be involved in guanidino-substrate recognition. R63A and R63Y mutants lost activity for taurocyamine, suggesting that these residues are associated with taurocyamine binding. In addition, we investigated the role of Tyr84 in D1 and found an association with substrate alignment. The Y84 residue was replaced with R, H, K, I, A, and G. Although the activities of each mutant were decreased (Vmax=2.36-67.50μmolPi/min/mgprotein), Y84 mutants possess binding affinity for taurocyamine (Km(Tauro)=3.19-10.04mM). The D1Y84R, D1Y84H, D1Y84K, and D1Y84A mutants exhibited low activity for taurocyamine, whereas the D1Y84I and D1Y84G mutants exhibited slightly decreased activity compared with the other Y84 mutants. The D1Y84K mutant lost substrate synergy between taurocyamine and ATP, suggesting that this mutation moves the position of the GS loop, similar to that of lombricine kinase (LK), and interferes with taurocyamine binding. This is the first comprehensive investigation of essential amino acid residues for substrate catalysis in trematode TK.
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Michibata J, Okazaki N, Motomura S, Uda K, Fujiwara S, Suzuki T. Two arginine kinases of Tetrahymena pyriformis: characterization and localization. Comp Biochem Physiol B Biochem Mol Biol 2014; 171:34-41. [PMID: 24726623 DOI: 10.1016/j.cbpb.2014.03.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 10/25/2022]
Abstract
Two cDNAs, one coding a typical 40-kDa arginine kinase (AK1) and the other coding a two-domain 80-kDa enzyme (AK2), were isolated from ciliate Tetrahymena pyriformis, and their recombinant enzymes were successfully expressed in Escherichia coli. Both enzymes had an activity comparable to those of typical invertebrate AKs. Interestingly, the amino acid sequence of T. pyriformis AK1, but not AK2, had a distinct myristoylation signal sequence at the N-terminus, suggesting that 40-kDa AK1 targets the membrane. Moreover, Western blot analysis showed that the AK1 is mainly localized in the ciliary fraction. Based on these results, we discuss the phosphoarginine shuttle, which enables a continuous energy flow to dynein for ciliary movement in T. pyriformis, and the role of AK1 in this model.
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Affiliation(s)
- Juri Michibata
- Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Noriko Okazaki
- Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Shou Motomura
- Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Kouji Uda
- Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Shigeki Fujiwara
- Cellular and Molecular Biotechnology, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Tomohiko Suzuki
- Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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11
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Folding Studies of Arginine Kinase from Euphausia superba Using Denaturants. Appl Biochem Biotechnol 2014; 172:3888-901. [DOI: 10.1007/s12010-014-0802-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 02/10/2014] [Indexed: 11/26/2022]
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12
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Palmer A, Begres BN, Van Houten JM, Snider MJ, Fraga D. Characterization of a putative oomycete taurocyamine kinase: Implications for the evolution of the phosphagen kinase family. Comp Biochem Physiol B Biochem Mol Biol 2013; 166:173-81. [PMID: 23978736 DOI: 10.1016/j.cbpb.2013.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 11/16/2022]
Abstract
Phosphagen kinases (PKs) are known to be distributed throughout the animal kingdom, but have recently been discovered in some protozoan and bacterial species. Within animal species, these enzymes play a critical role in energy homeostasis by catalyzing the reversible transfer of a high-energy phosphoryl group from Mg⋅ATP to an acceptor molecule containing a guanidinium group. In this work, a putative PK gene was identified in the oomycete Phytophthora sojae that was predicted, based on sequence homology, to encode a multimeric hypotaurocyamine kinase. The recombinant P. sojae enzyme was purified and shown to catalyze taurocyamine phosphorylation efficiently (kcat/KM (taurocyamine) = 2 × 10(5) M(-1) s(-1)) and glycocyamine phosphorylation only weakly (kcat/KM (glycocyamine) = 2 × 10(2) M(-1) s(-1)), but lacked any observable kinase activity with the more ubiquitous guanidinium substrates, creatine or arginine. Additionally, the enzyme was observed to be dimeric but lacked cooperativity between the subunits in forming a transition state analog complex. These results suggest that protozoan PKs may exhibit more diversity in substrate specificity than was previously thought.
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Affiliation(s)
- Allyson Palmer
- Program in Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH 44691, USA
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Jarilla BR, Tokuhiro S, Nagataki M, Uda K, Suzuki T, Acosta LP, Agatsuma T. Gene structure of the two-domain taurocyamine kinase from Paragonimus westermani: evidence for a distinct lineage of trematode phosphagen kinases. FEBS Lett 2013; 587:2278-83. [PMID: 23751729 DOI: 10.1016/j.febslet.2013.05.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/19/2013] [Accepted: 05/29/2013] [Indexed: 11/17/2022]
Abstract
Taurocyamine kinase (TK) is an enzyme that catalyzes the reversible transfer of a phosphate between ATP and taurocyamine. Annelid TKs were suggested to have evolved from a CK ancestor. However, TKs from the lung fluke Paragonimus westermani comprised another lineage. Construction of phylogenetic tree and comparison of exon/intron organization showed that P. westermani TK and other trematode TKs evolved from a molluscan arginine kinase (AK) gene. Exon shuffling probably caused the changes in amino acid sequence thereby changing the affinity from AK to TK. The present study provides new insights on the evolution of phosphagen kinases found in trematodes.
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Affiliation(s)
- Blanca R Jarilla
- Department of Environmental Health Sciences, Kochi University, Kochi 783-8505, Japan
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14
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Phosphagen kinase in Schistosoma japonicum: characterization of its enzymatic properties and determination of its gene structure. Mol Biochem Parasitol 2013; 188:91-8. [PMID: 23603791 DOI: 10.1016/j.molbiopara.2013.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/11/2013] [Accepted: 04/09/2013] [Indexed: 11/22/2022]
Abstract
Phosphagen kinases (PKs) play a major role in the regulation of energy metabolism in animals. Creatine kinase (CK) is the sole PK in vertebrates, whereas several PKs are present in invertebrates. Here, we report the enzymatic properties and gene structure of PK in the trematode Schistosoma japonicum (Sj). SjPK has a unique contiguous dimeric structure comprising domain 1 (D1) and domain 2 (D2). The three states of the recombinant SjPK (D1, D2, and D1D2) show a specific activity for the substrate taurocyamine. The comparison of the two domains of SjPK revealed that D1 had a high turnover rate (kcat=52.91) and D2 exhibited a high affinity for taurocyamine (Km(Tauro) =0.53±0.06). The full-length protein exhibited higher affinity for taurocyamine (Km(Tauro) =0.47±0.03) than the truncated domains (D1=1.30±0.10, D2=0.53±0.06). D1D2 also exhibited higher catalytic efficiency (kcat/Km(Tauro) =82.98) than D1 (40.70) and D2 (29.04). These results demonstrated that both domains of SjTKD1D2 interacted efficiently and remained functional. The three-dimensional structure of SjPKD1 was constructed by the homology modeling based on the transition state analog complex state of Limulus AK. This protein model of SjPKD1 suggests that the overall structure is almost conserve between SjPKD1 and Limulus AK except for the flexible loops, that is, particularly guanidino-specificity (GS) region, which is associated with the recognition of the corresponding guanidino substrate. The constructed NJ tree and the comparison of exon/intron organization suggest that SjTK has evolved from an arginine kinase (AK) gene. SjTK has potential as a novel antihelminthic drug target as it is absent in mammals and its strong activity may imply a significant role for this protein in the energy metabolism of the parasite.
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15
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Uda K, Hoshijima M, Suzuki T. A novel taurocyamine kinase found in the protist Phytophthora infestans. Comp Biochem Physiol B Biochem Mol Biol 2013; 165:42-8. [PMID: 23499944 DOI: 10.1016/j.cbpb.2013.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/05/2013] [Accepted: 03/05/2013] [Indexed: 11/30/2022]
Abstract
Phosphagen kinase (PK), which is typically in the form of creatine kinase (CK; EC 2.7.3.2) in vertebrates or arginine kinase (AK; EC 2.7.3.3) in invertebrates, plays a key role in ATP buffering systems of tissues and nerves that display high and variable rates of ATP turnover. The enzyme is also found with intermittent occurrence as AK in unicellular organisms, protist and bacteria species, suggesting an ancient origin of AK. Through a database search, we identified two novel PK genes, coding 40- and 80-kDa (contiguous dimer) enzymes in the protist Phytophthora infestans. Both enzymes showed strong activity for taurocyamine and, in addition, we detected taurocyamine in cell extracts of P. infestans. Thus, the enzyme was identified to be taurocyamine kinase (TK; EC 2.7.3.4). This was the first phosphagen kinase, other than AK, to be found in unicellular organisms. Their position on the phylogenetic tree indicates that P. infestans TKs evolved uniquely at an early stage of evolution. Occurrence of TK in protists suggests that PK enzymes show flexible substrate specificity.
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Affiliation(s)
- Kouji Uda
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
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16
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Suzuki T, Yamamoto K, Tada H, Uda K. Cold-adapted features of arginine kinase from the deep-sea clam Calyptogena kaikoi. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:294-303. [PMID: 22016076 DOI: 10.1007/s10126-011-9411-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 09/29/2011] [Indexed: 05/31/2023]
Abstract
The heterodont clam Calyptogena kaikoi, which inhabits depths exceeding 3,500 m where low ambient temperatures prevail, has an unusual two-domain arginine kinase (AK) with molecular mass of 80 kDa, twice that of typical AKs. The purpose of this work is to investigate the nature of the adaptations of this AK for functioning at low temperatures. Recombinant C. kaikoi AK constructs were expressed, and their two-substrate kinetic constants (k(cat), K(a), and K(ia)) were determined at 10°C and 25°C, respectively. When measured at 25°C, the K(ia) values were tenfold larger than those for corresponding K(a) values, while at 10°C, the K(ia) values decreased remarkably, but the K (a) values were almost unchanged. The Calyptogena two-domain enzyme has threefold higher catalytic efficiency, calculated by k (cat)/(K(a)(ARG)·K(ia)(ATP) ), at 10°C, than that at 25°C, reflecting adaptation for function at reduced ambient temperatures. The activation energy (E(a)) and thermodynamic parameters were determined for Calyptogena two-domain enzyme and compared with those of two-domain enzymes from mesophilic Corbicula and Anthopleura. The value for E(a) of Calyptogena enzyme were about half of those for mesophilic enzymes, and a larger decrease in entropy was observed in Calyptogena AK reaction. Although large decrease in entropy increases the ΔG(o‡) value and consequently lowers the k(cat) value, this is compensated with its lower E(a) value thereby minimizing the reduction in its k(cat) value. These thermodynamic properties, together with the kinetic ones, are also present in the separated domain 2 of the Calyptogena two-domain enzyme.
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Affiliation(s)
- Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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17
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Uda K, Ellington WR, Suzuki T. A diverse array of creatine kinase and arginine kinase isoform genes is present in the starlet sea anemone Nematostella vectensis, a cnidarian model system for studying developmental evolution. Gene 2012; 497:214-27. [PMID: 22305986 DOI: 10.1016/j.gene.2012.01.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 01/16/2012] [Accepted: 01/19/2012] [Indexed: 11/25/2022]
Abstract
Phosphagen (guanidino) kinases (PK) constitute a family of homologous phosphotransferases catalyzing the reversible transfer of the high-energy phosphoryl group of ATP to naturally occurring guanidine compounds. Prior work has shown that PKs can be phylogenetically separated into two distinct groups- an arginine kinase (AK) subfamily and a creatine kinase (CK) subfamily. The latter includes three CK isoforms- cytoplasmic CK (CyCK), mitochondrial CK (MiCK) and three-domain flagellar CK (fCK). In the present study we identified six unique PK genes from the draft genome sequence of the starlet sea anemone Nematostella vectensis, a well-known model organism for understanding metazoan developmental evolution. Using reverse transcription polymerase chain reaction (RTPCR) methods, full length cDNAs were amplified for all of these PKs. These cDNAs were cloned and expressed in Escherichia coli as 6x His-tagged fusion proteins. The six PKs were identified as the three typical CK isoforms (CyCK, MiCK and fCK), two unusual AKs (a two-domain AK (2DAK) and a three-domain AK (3DAK)) and a PK which phosphorylated arginine. The latter enzyme had a very low AK activity (its apparent V(max) value being less than 0.2% that of 3DAK), lacks several key residues necessary for AK enzyme activity, and was tentatively designated as AK1. As far as we know, this constitutes the first report of an AK with the three fused AK domains. The Bayesian tree suggested that the third domain of 3DAK likely evolved from the gene for domain 2 of typical two-domain AK found widely in cnidarians. Construction of phylogenetic trees and comparison of exon-intron organizations of their respective genes indicated that the N. vectensis three-domain fCK and 3DAK evolved independently, and both enzymes are likely to be targeted to cell membranes since they have a myristoylation signal at their respective N-termini. These results complement prior work on other basal invertebrates showing that multiple CK and AK isoform genes were present at the dawn of the radiation of metazoans. The presence of isoform diversity in an organism lacking in structural complexity reflects an early imperative for targeting of PKs to particular cellular contexts such as muscle fibers, neurons, ciliated/flagellated epithelia and spermatozoa.
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18
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Wu QY, Li F, Wang XY, Chen ZJ. Impact of inter-subunit interactions on the dimeric arginine kinase activity and structural stability. Arch Biochem Biophys 2011; 512:61-8. [PMID: 21549684 DOI: 10.1016/j.abb.2011.04.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/20/2011] [Accepted: 04/22/2011] [Indexed: 11/19/2022]
Abstract
Arginine kinase (AK) is a key enzyme for cellular energy metabolism, catalyzing the reversible phosphoryl transfer from phosphoarginine to ADP in invertebrates. In this study, the inter-subunit hydrogen bonds between the Q53 and D200 and between D57 and D200 were disrupted to explore their roles in the activity and structural stability of Stichopus japonicus (S. japonicus) AK. Mutating Q53 and/or D57 to alanine (A) can cause pronounced loss of activity and substrate synergism, and cause distinct conformational changes. Spectroscopic experiments indicated that mutations destroying the inter-subunit hydrogen bonds impaired the structure of dimer AK, and resulted in a partially unfolded state. The inability to fold to the functional compact state made the mutants prone to be inactivated and aggregate under environmental stresses. Restoring hydrogen bonds in Q53E and D57E mutants could rescue the loss of activity and substrate synergism, and conformational changes. All those results suggested that the inter-subunit interactions played a key role in keeping the activity, substrate synergism and structural stability of dimer AK. The result herein may provide a clue in understanding the folding and self-assembly processes of oligomeric proteins.
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Affiliation(s)
- Qing-Yun Wu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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19
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Uda K, Ishida M, Matsui T, Suzuki T. Arginine Kinase from the Tardigrade, Macrobiotus occidentalis: Molecular Cloning, Phylogenetic Analysis and Enzymatic Properties. Zoolog Sci 2010; 27:796-803. [DOI: 10.2108/zsj.27.796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Cooperativity in the two-domain arginine kinase from the sea anemone Anthopleura japonicus. II. Evidence from site-directed mutagenesis studies. Int J Biol Macromol 2010; 47:250-4. [DOI: 10.1016/j.ijbiomac.2010.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 04/17/2010] [Accepted: 04/22/2010] [Indexed: 11/20/2022]
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21
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Evolution of double MutT/Nudix domain-containing proteins: similar domain architectures from independent gene duplication-fusion events. J Genet Genomics 2009; 36:603-10. [DOI: 10.1016/s1673-8527(08)60152-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 02/26/2009] [Accepted: 03/12/2009] [Indexed: 11/21/2022]
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22
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Jarilla BR, Tokuhiro S, Nagataki M, Hong SJ, Uda K, Suzuki T, Agatsuma T. Molecular characterization and kinetic properties of a novel two-domain taurocyamine kinase from the lung flukeParagonimus westermani. FEBS Lett 2009; 583:2218-24. [DOI: 10.1016/j.febslet.2009.05.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 05/19/2009] [Accepted: 05/28/2009] [Indexed: 11/25/2022]
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23
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Weiss C, Bonshtien A, Farchi-Pisanty O, Vitlin A, Azem A. Cpn20: siamese twins of the chaperonin world. PLANT MOLECULAR BIOLOGY 2009; 69:227-38. [PMID: 19031045 DOI: 10.1007/s11103-008-9432-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 11/08/2008] [Indexed: 05/08/2023]
Abstract
The chloroplast cpn20 protein is a functional homolog of the cpn10 co-chaperonin, but its gene consists of two cpn10-like units joined head-to-tail by a short chain of amino acids. This double protein is unique to plastids and was shown to exist in plants as well plastid-containing parasites. In vitro assays showed that this cpn20 co-chaperonin is a functional homolog of cpn10. In terms of structure, existing data indicate that the oligomer is tetrameric, yet it interacts with a heptameric cpn60 partner. Thus, the functional oligomeric structure remains a mystery. In this review, we summarize what is known about this distinctive chaperonin and use a bioinformatics approach to examine the expression of cpn20 in Arabidopsis thaliana relative to other chaperonin genes in this species. In addition, we examine the primary structure of the two homologous domains for similarities and differences, in comparison with cpn10 from other species. Lastly, we hypothesize as to the oligomeric structure and raison d'être of this unusual co-chaperonin homolog.
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Affiliation(s)
- Celeste Weiss
- Department of Biochemistry, Tel Aviv University, Tel Aviv, Israel
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24
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Wang H, Zhang L, Zhang L, Lin Q, Liu N. Arginine kinase: differentiation of gene expression and protein activity in the red imported fire ant, Solenopsis invicta. Gene 2008; 430:38-43. [PMID: 19028554 DOI: 10.1016/j.gene.2008.10.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 10/01/2008] [Accepted: 10/16/2008] [Indexed: 11/24/2022]
Abstract
Arginine kinase (AK), a primary enzyme in cell metabolism and adenosine 5'-triphosphate (ATP)-consuming processes, plays an important role in cellular energy metabolism and maintaining constant ATP levels in invertebrate cells. In order to identify genes that are differentially expressed between larvae and adults, queens and workers, and female alates (winged) and queens (wingless), AK cDNA was obtained from the red imported fire ant. The cDNA sequence of the gene has open reading frames of 1065 nucleotides, encoding a protein of 355 amino acid residues that includes the substrate recognition region, the signature sequence pattern of ATP:guanidino kinases, and an "actinin-type" actin binding domain. Northern blot analysis and protein activity analysis demonstrated that the expression of the AK gene and its protein activity were developmentally, caste specifically, and tissue specifically regulated in red imported fire ants with a descending order of worker> alate (winged adult) female> alate (winged adult) male> larvae> worker pupae approximately alate pupae. These results suggest a different demand for energy-consumption and production in the different castes of the red imported fire ant, which may be linked to their different missions and physiological activities in the colonies. The highest level of the AK gene expression and activity was identified in head tissue of both female alates and workers and thorax tissue of workers, followed by thorax tissue of female alates and abdomen tissue of male alates, suggesting the main tissues or cells in these body parts, such as brain, neurons and muscles, which have been identified as the major tissues and/or cells that display high and variable rates of energy turnover in other organisms, play a key role in energy production and its utilization in the fire ant. In contrast, in the male alate, the highest AK expression and activity were found in the abdomen, suggesting that here energy demand may relate to sperm formation and reproduction.
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Affiliation(s)
- Haichuan Wang
- Department of Entomology and Plant Pathology, 301 Funchess Hall, Auburn University, Auburn, AL 36849-5413, USA
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25
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Song KH, Jung MK, Eum JH, Hwang IC, Han SS. Proteomic analysis of parasitized Plutella xylostella larvae plasma. JOURNAL OF INSECT PHYSIOLOGY 2008; 54:1270-1280. [PMID: 18671979 DOI: 10.1016/j.jinsphys.2008.06.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 06/20/2008] [Accepted: 06/20/2008] [Indexed: 05/26/2023]
Abstract
Insects use their innate immunity to defend themselves against foreign invaders, such as microorganisms, nematodes and parasites. Cotesia plutellae, an endoparasitoid wasp that parasitizes the diamondback moth Plutella xylostella, uses several strategies to attack the host immune system, such as injection of viruses, venom, and serosal membrane-derived cells denoted teratocytes. However, the proteome profiles related to these immune deficiency systems have yet to be clearly defined. In this study, we investigate differences in protein expression patterns in parasitized P. xylostella larvae, with a view to identifying parasitism-specific factors. Using 2D polyacrylamide gel electrophoresis, proteins in the host plasma were assessed every 48 h after parasitism by C. plutellae. A large number of protein spots (350 in total) were detected, and approximately 50 spots were differentially expressed in the parasitized P. xylostella larvae every 48 h. In total, 26 potential candidates, including P. xylostella Serpin 2 (pxSerpin 2), translationally controlled tumor protein, signal transduction histidine kinase, apolipophorin-III, and fatty-acid binding protein were identified through quadrupole time-of-flight tandem mass spectrometry and sequence homology analysis. These proteins were classified into the following functional groups: immunity, signaling, lipid metabolism, energy metabolism, amino acid/nucleotide metabolism, and others. The pxSerpin 2 gene was cloned, and its expression profile investigated during the course of parasitism. Real-time PCR analysis of pxSerpin 2 revealed a poor correlation between the mRNA level and protein abundance. Our results clearly suggest that parasitism-specific proteins participate in suppression of the host immune response.
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Affiliation(s)
- Kyung-Han Song
- School of Life Science and Biotechnology, Korea University, Seoul 136-701, Republic of Korea
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26
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Uda K, Yamamoto K, Iwasaki N, Iwai M, Fujikura K, Ellington WR, Suzuki T. Two-domain arginine kinase from the deep-sea clam Calyptogena kaikoi--evidence of two active domains. Comp Biochem Physiol B Biochem Mol Biol 2008; 151:176-82. [PMID: 18639645 DOI: 10.1016/j.cbpb.2008.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Revised: 06/24/2008] [Accepted: 06/25/2008] [Indexed: 11/18/2022]
Abstract
The cDNA and deduced amino acid sequences for arginine kinase (AK) from the deep-sea clam Calyptogena kaikoi have been determined revealing an unusual two-domain (2D) structure with molecular mass of 80 kDa, twice that of normal AK. The amino acid sequences of both domains contain most of the residues thought to be required for substrate binding found in the horseshoe crab Limulus polyphemus AK, a well studied system for which several X-ray crystal structures exist. However, two highly conserved residues, D62 and R193, that form a salt bridge thereby stabilizing the substrate-bound structure have been replaced by G and N in domain 1, and G and P in domain 2, respectively. The present effort probes whether both domains of Calyptogena AK are catalytically competent. Recombinant constructs of the wild-type enzyme of both single domains, and of selected mutants of the Calyptogena AK have been expressed as fusion proteins with the maltose-binding protein. The wild-type two-domain enzyme (2D[WT]) had high AK activity (k(cat)=23 s(- 1), average value of the two domains), and the single domain 2 (D2[WT]) showed 1.5-times higher activity (k(cat)=38 s(- 1)) than the wild-type 2D[WT]. Interestingly, the single domain 1 (D1[WT]) showed only a very low activity (k(cat) approximately 0.016 s(- 1)). Introduction of a Y68A mutation in both domains virtually abolished catalytic activity. On the other hand, significant residual activity was observed (k(cat)=2.8 s(- 1)), when the Y68A mutation was introduced only into domain 2 of the two-domain enzyme. A similar mutation in domain 1 of the two-domain enzyme reduced activity to a much lower extent (k(cat)=11.1 s(- 1)). Although the domains of this "contiguous" dimeric AK each have catalytic capabilities, the presence of domain 2 strongly influences the stability and activity of domain 1.
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Affiliation(s)
- Kouji Uda
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
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27
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Hoffman GG, Davulcu O, Sona S, Ellington WR. Contributions to catalysis and potential interactions of the three catalytic domains in a contiguous trimeric creatine kinase. FEBS J 2008; 275:646-54. [PMID: 18190534 DOI: 10.1111/j.1742-4658.2007.06226.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three separate creatine kinase (CK) isoform families exist in animals. Two of these (cytoplasmic and mitochondrial) are obligate oligomers. A third, flagellar, is monomeric but contains the residues for three complete CK domains. It is not known whether the active sites in each of the contiguous flagellar domains are catalytically competent, and, if so, whether they are capable of acting independently. Here we have utilized site-directed mutagenesis to selectively disable individual active sites and all possible combinations thereof. Kinetic studies showed that these mutations had minimal impact on substrate binding and synergism. Interestingly, the active sites were not catalytically equivalent, and were in fact interdependent, a phenomenon that has previously been reported only in the oligomeric CK isoforms.
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Affiliation(s)
- Gregg G Hoffman
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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28
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Tada H, Nishimura Y, Suzuki T. Cooperativity in the two-domain arginine kinase from the sea anemone Anthopleura japonicus. Int J Biol Macromol 2008; 42:46-51. [DOI: 10.1016/j.ijbiomac.2007.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Revised: 09/11/2007] [Accepted: 09/11/2007] [Indexed: 10/22/2022]
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29
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Abstract
We determined the cDNA-derived amino acid sequences of two arginine kinases (AK1, AK2) from the annelid Sabellastarte indica, cloned the cDNAs into pMAL plasmid and expressed them in E. coli. The phylogenetic analyses suggested that Sabellastarte AKs have evolved from a CK-related gene, not from the usual AK gene. The recombinant Sabellastarte AK1 showed a broad specificity towards various guanidine compounds, while the Sabellastarte AK2 mainly showed stronger activity for both D- and L-arginine, a very unique substrate specificity not seen before in usual AKs. We isolated guanidino compounds from the body wall musculature of Sabellastarte, and found that the major compound is D-arginine with a concentration of 4.85 +/- 0.51 mmol/kg. From these results, we suggest strongly that in Sabellastarte, D-arginine is the major phosphagen substrate and that the AK2 with substrate specificity towards D-arginine, catalyzes the phosphorylation of D-arginine.
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Affiliation(s)
- Kouji Uda
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi, 780-8520, Japan
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30
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Jourden MJ, Clarke CN, Palmer AK, Barth EJ, Prada RC, Hale RN, Fraga D, Snider MJ, Edmiston PL. Changing the substrate specificity of creatine kinase from creatine to glycocyamine: evidence for a highly evolved active site. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1519-27. [PMID: 17976392 DOI: 10.1016/j.bbapap.2007.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 10/01/2007] [Accepted: 10/02/2007] [Indexed: 11/16/2022]
Abstract
Eight variants of creatine kinase were created to switch the substrate specificity from creatine to glycocyamine using a rational design approach. Changes to creatine kinase involved altering several residues on the flexible loops that fold over the bound substrates including a chimeric replacement of the guanidino specificity loop from glycocyamine kinase into creatine kinase. A maximal 2,000-fold change in substrate specificity was obtained as measured by a ratio of enzymatic efficiency (k(cat)/K(M).K(d)) for creatine vs. glycocyamine. In all cases, a change in specificity was accompanied by a large drop in enzymatic efficiency. This data, combined with evidence from other studies, indicate that substrate specificity in the phosphagen kinase family is obtained by precise alignment of substrates in the active site to maximize k(cat)/K(M).K(d) as opposed to selective molecular recognition of one guanidino substrate over another. A model for the evolution of the dimeric forms of phosphagen kinases is proposed in which these enzymes radiated from a common ancestor that may have possessed a level of catalytic promiscuity. As mutational events occurred leading to greater degrees of substrate specificity, the dimeric phosphagen kinases became evolutionary separated such that the substrate specificity could not be interchanged by a small number of mutations.
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Affiliation(s)
- Michael J Jourden
- Department of Chemistry, College of Wooster, 943 College Mall, Wooster, OH 44691, USA
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31
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Held BC, Wright-Weber B, Grossman SH. Kinetic analysis of two purified forms of arginine kinase: absence of cooperativity in substrate binding of dimeric phosphagen kinase. Comp Biochem Physiol B Biochem Mol Biol 2007; 148:6-13. [PMID: 17572125 DOI: 10.1016/j.cbpb.2007.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 03/19/2007] [Accepted: 03/26/2007] [Indexed: 10/23/2022]
Abstract
Arginine kinase from sea urchin eggs and sea cucumber muscle are dimeric enzymes, unlike the more widely distributed monomeric enzyme found in other invertebrates. Both purified enzymes exhibited features characteristic of the monomeric arginine kinases including pH optima, formation of a catalytic dead-end complex (enzyme-MgADP-arginine) and stabilization of this complex by monovalent anions. A complete analysis of initial velocity data, in both directions for each substrate, indicated that substrate binding cooperativity was either minimal or non-existent. Unlike many other multi-subunit enzymes, the significance of the dimeric state of the phosphagen kinases remains unclear. These present results would suggest that (a) cooperativity, or so-called synergism in substrate binding is not a characteristic of the dimeric state of the protein and (b) the functional significance of the dimeric state is not related to the ability of some of these enzymes to undergo cooperativity in substrate binding. The significance of the dimeric state for the creatine kinases and arginine kinases remains to be established.
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Affiliation(s)
- Brenda C Held
- University of South Florida, Department of Chemistry, 4202 East Fowler Avenue Tampa, FL 33620, USA
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Tanaka K, Ichinari S, Iwanami K, Yoshimatsu S, Suzuki T. Arginine kinase from the beetle Cissites cephalotes (Olivier). Molecular cloning, phylogenetic analysis and enzymatic properties. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2007; 37:338-45. [PMID: 17368197 DOI: 10.1016/j.ibmb.2006.12.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Revised: 12/13/2006] [Accepted: 12/20/2006] [Indexed: 05/14/2023]
Abstract
Here, we report the PCR amplification and cloning of a cDNA for arginine kinase (AK) from the beetle Cissites cephalotes (Olivier). The cDNA is 1210bp and has an open reading frame of 1125bp and 5' and 3'-untranslated regions of 30 and 55bp, respectively. The open reading frame encodes a 374 amino acid protein with most of the residues considered necessary for AK function: five residues predicted to interact with the substrate arginine (S77, Y82, E239, C285 and E328), and five residues predicted to interact with the substrate ADP (R138, R140, R243, R294 and R323). A phylogenetic tree of arthropod AKs indicated clearly that insect AKs can be separated into typical AKs from various insect species (group 1) and putative AK sequences deduced from genomic sequences (group 2). Cissites AK clustered in group 2 and provides the first evidence that a group-2 gene is indeed expressed in insects. Moreover, we expressed Cissites AK protein in Escherichia coli as a fusion with maltose-binding protein, and kinetic constants (K(m), K(d), V(max) and k(cat)) were determined for the forward reaction. Comparison of kinetic constants with those of AKs from other sources (insects, mollusks and echinoderms) indicated that insect AKs from Cissites and Periplaneta have two very unique features, the lowest k(cat) (and k(cat)/K(m)(arg)) among AKs, and a lack of synergistic substrate binding (K(d)/K(m) approximately 1).
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Affiliation(s)
- Kumiko Tanaka
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
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Uda K, Fujimoto N, Akiyama Y, Mizuta K, Tanaka K, Ellington WR, Suzuki T. Evolution of the arginine kinase gene family. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2005; 1:209-18. [PMID: 20483252 DOI: 10.1016/j.cbd.2005.10.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 10/25/2005] [Accepted: 10/26/2005] [Indexed: 12/16/2022]
Abstract
Arginine kinase (AK), catalyzing the reversible transfer of phosphate from MgATP to arginine yielding phosphoarginine and MgADP, is widely distributed throughout the invertebrates and is also present in certain protozoa. Typically, these proteins are found as monomers targeted to the cytoplasm, but true dimeric and contiguous dimeric AKs as well as mitochondrial AK activities have been observed. In the present study, we have obtained the sequences of the genes for AKs from two distantly related molluscs-the cephalopod Nautilus pompilius and the bivalve Crassostrea gigas. These new data were combined with available gene structure data (exon/intron organization) extracted from EST and genome sequencing project databases. These data, comprised of 23 sequences and gene structures from Protozoa, Cnidaria, Platyhelminthes, Mollusca, Arthropoda and Nematoda, provide great insight into the evolution and divergence of the AK family. Sequence and phylogenetic analyses clearly show that the AKs are homologous having arisen from some common ancestor. However, AK gene organization is highly divergent and variable. Molluscan AK genes typically have a highly conserved six-exon/five-intron organization, a structure that is very similar to that of the platyhelminth Schistosoma mansoni Arthropod and nematode AK genes have fewer introns, while the cnidarian and protozoan genes each display unique exon/intron organization when compared to the other AK genes. The non-conservative nature of the AK genes is in sharp contrast to the relatively high degree of conservation of intron positions seen in a homologous enzyme creatine kinase (CK). The present results also show that gene duplication and subsequent fusion events forming unusual two-domain AKs occurred independently at least four times as these contiguous dimers are present in Protozoa, Cnidaria, Platyhelminthes and Mollusca. Detailed analyses of the amino acid sequences indicate that two AKs (one each from Drosophila and Caenorhabditis) have what appear to be N-terminal mitochondrial targeting sequences, providing the first evidence for true mitochondrial AK genes. The AK gene family is ancient and the lineage has undergone considerable divergence as well as multiple duplication and fusion events.
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Affiliation(s)
- Kouji Uda
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
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Abstract
Found in all vertebrates, creatine kinase catalyzes the reversible reaction of creatine and ATP forming phosphocreatine and ADP. Phosphocreatine may be viewed as a reservoir of "high-energy phosphate" which is able to supply ATP, the primary energy source in bioenergetics, on demand. Consequently, creatine kinase plays a significant role in energy homeostasis of cells with intermittently high energy requirements. The enzyme is of clinical importance and its levels are routinely used as an indicator of myocardial and skeletal muscle disorders and for the diagnosis of acute myocardial infarction. First identified in 1928, the enzyme has undergone intensive investigation for over 75 years. There are four major isozymes, two cytosolic and two mitochondrial, which form dimers and octamers, respectively. Depending on the pH, the enzyme operates by a random or an ordered bimolecular mechanism, with the equilibrium lying towards phosphocreatine production. Evidence suggests that conversion of creatine to phosphocreatine occurs via the in-line transfer of a phosphoryl group from ATP. A recent X-ray structure of creatine kinase bound to a transition state analog complex confirmed many of the predictions based on kinetic, spectroscopic, and mutagenesis studies. This review summarizes and correlates the more significant mechanistic and structural studies on creatine kinase.
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Leggat W, Dixon R, Saleh S, Yellowlees D. A novel carbonic anhydrase from the giant clam Tridacna gigas contains two carbonic anhydrase domains. FEBS J 2005; 272:3297-305. [PMID: 15978036 DOI: 10.1111/j.1742-4658.2005.04742.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This report describes the presence of a unique dual domain carbonic anhydrase (CA) in the giant clam, Tridacna gigas. CA plays an important role in the movement of inorganic carbon (Ci) from the surrounding seawater to the symbiotic algae that are found within the clam's tissue. One of these isoforms is a glycoprotein which is significantly larger (70 kDa) than any previously reported from animals (generally between 28 and 52 kDa). This alpha-family CA contains two complete carbonic anhydrase domains within the one protein, accounting for its large size; dual domain CAs have previously only been reported from two algal species. The protein contains a leader sequence, an N-terminal CA domain and a C-terminal CA domain. The two CA domains have relatively little identity at the amino acid level (29%). The genomic sequence spans in excess of 17 kb and contains at least 12 introns and 13 exons. A number of these introns are in positions that are only found in the membrane attached/secreted CAs. This fact, along with phylogenetic analysis, suggests that this protein represents the second example of a membrane attached invertebrate CA and it contains a dual domain structure unique amongst all animal CAs characterized to date.
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Affiliation(s)
- William Leggat
- Biochemistry and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
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Fujimoto N, Tanaka K, Suzuki T. Amino acid residues 62 and 193 play the key role in regulating the synergism of substrate binding in oyster arginine kinase. FEBS Lett 2005; 579:1688-92. [PMID: 15757662 DOI: 10.1016/j.febslet.2005.02.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Revised: 02/01/2005] [Accepted: 02/03/2005] [Indexed: 11/22/2022]
Abstract
The purpose of this study is to clarify the amino acid residues responsible for the synergism in substrate binding of arginine kinase (AK), a key enzyme in invertebrate energy metabolism. AKs contain a pair of highly conserved amino acids (D62 and R193) that form an ion pair, and replacement of these residues can cause a pronounced loss of activity. Interestingly, in the oyster Crassostrea AK, these residues are replaced by an N and a K, respectively. Despite this replacement, the enzyme retains high activity and moderate synergism in substrate binding (Kd/Km=2.3). We replaced the N62 by G or D and the K193 by G or R in Crassostrea AK, and also constructed the double mutants of N62G/K193G and N62D/K193R. All of the mutants retained 50-90% of the wild-type activity. In N62G and N62D mutants, the Kmarg for arginine binding was comparable to that of wild-type enzyme, but the Kdarg was increased 2-5-fold, resulting in a strong synergism (Kd/Km=4.9-11.3). On the other hand, in K193G and K193R mutants, the Kmarg was increased 4-fold, and synergism was lost almost completely (Kd/Km=1.0-1.4). The N62G/K193G double mutant showed similar characteristics to the K193G and K193R mutants. Another double mutant, N62D/K193R, similar to the amino acid pair in the wild-type enzyme, had characteristics similar to those of the wild-type enzyme. These results indicate that the amino acid residues 62 and 193 play the key role in mediating the synergism in substrate binding of oyster arginine kinase.
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Affiliation(s)
- Naka Fujimoto
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
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Pan JC, Yu ZH, Hui EF, Zhou HM. Conformational change and inactivation of arginine kinase from shrimp Feneropenaeus chinensis in oxidized dithiothreitol solutions. Biochem Cell Biol 2005; 82:361-7. [PMID: 15181469 DOI: 10.1139/o04-033] [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: 11/22/2022] Open
Abstract
The effect of oxidized dithiothreitol (DTT) on the conformation and function of arginine kinase from shrimp Feneropenaeus chinensis was investigated with the methods of intrinsic fluorescence, ANS fluorescence, size exclusion chromatography (SEC), sodium dodecyl sulfate - polyacrylamide gel electrophoresis (SDS-PAGE), and activity assay. The excess molecular oxidized dithiothreitol could result in a loss of activity and conformational change of arginine kinase. The oxidized arginine kinase was characterized by monitoring the changes of fluorescence emission wavelength (excitation wavelength: 295 nm) and the intensity of 1-anilino-8-naphthalenesulfonate (ANS) binding (excitation wavelength: 380 nm) to the protein. The results of fluorescence spectra showed that the presence of oxidized DTT could result in a marked change in the enzyme tertiary structure. The conformational changes of native and oxidized arginine kinase are induced by the presence of the full set of transition state analog (TSA) components. The results of size exclusion chromatography and SDS-PAGE indicated that no disulfide bond was formed among the protein molecules in the oxidized-DTT solution.
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Affiliation(s)
- Ji-Cheng Pan
- Department of Biological Science and Biotechnology, Tsinghua University, Beijing 100084, People's Republic of China
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Pan JC, Cheng Y, Hui EF, Zhou HM. Implications of the role of reactive cystein in arginine kinase: reactivation kinetics of 5,5′-dithiobis-(2-nitrobenzoic acid)-modified arginine kinase reactivated by dithiothreitol. Biochem Biophys Res Commun 2004; 317:539-44. [PMID: 15063791 DOI: 10.1016/j.bbrc.2004.03.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Indexed: 11/27/2022]
Abstract
The reduction of 5,5'-dithiobis-(2-nitrobenzoic acid)-modified arginine kinase by dithiothreitol has been investigated using the kinetic theory of the substrate reaction during modification of enzyme activity. The results show that the modified arginine kinase can be fully reactivated by an excess concentration of dithiothreitol in a monophasic kinetic course. The presence of ATP or the transition-state analog markedly slows the apparent reactivation rate constant, while arginine shows no effect. The results of ultraviolet (UV) difference and intrinsic fluorescence spectra indicate that the substrate arginine-ADP-Mg2+ can induce conformational changes of the modified enzyme but adding NO3- cannot induce further changes that occur with the native enzyme. The reactive cysteines' location and role in the catalysis of arginine kinase are discussed. It is suggested that the cysteine may be located in the hinge region of the two domains of arginine kinase. The reactive cysteine of arginine kinase may play an important role not in the binding to the transition-state analog but in the conformational changes caused by the transition-state analog.
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Affiliation(s)
- Ji-Cheng Pan
- Department of Biological Science and Biotechnology, Tsinghua University, Beijing 100084, PR China
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39
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Compaan DM, Ellington WR. Functional consequences of a gene duplication and fusion event in an arginine kinase. J Exp Biol 2003; 206:1545-56. [PMID: 12654893 DOI: 10.1242/jeb.00299] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Arginine kinase (AK) from the foot of the razor clam Ensis directus consists of two full-length AK domains, denoted D1 and D2, fused in a single polypeptide chain. The full-length cDNA for Ensis AK was obtained and its deduced amino acid sequence was analyzed in the context of the X-ray crystal structure of a typical, monomeric AK. Both domains of Ensis AK contain most of the residues currently thought to be critical in catalysis, suggesting that both AK domains are catalytically competent. The full-length Ensis AK, a D2-NusA-His-tag fusion protein and a D2-truncated AK (enterokinase cleavage product of the fusion protein) were expressed in Escherichia coli and purified. All recombinant AK constructs displayed high enzyme activity. Attempts at expressing active D1 alone, D2 alone or a D1-NusA-His-tag fusion protein were unsuccessful. The catalytic properties of the active proteins were compared with the corresponding properties of recombinant AK from the horseshoe crab Limulus polyphemus, which is a typical monomeric AK. In contrast to expectations, the kinetic results strongly suggest that Ensis AK has only one active domain, namely D2. The K(cat) values for all Ensis constructs were roughly twice that of typical AKs, indicating higher overall catalytic throughput at the competent active site. Furthermore, both the full-length and truncated D2 Ensis AKs showed no synergism of substrate binding unlike typical AKs. The D2-NusA-His-tag fusion construct actually displayed negative synergism of substrate binding, which means that, in effect, the first substrate bound acts as a competitive inhibitor of the second. The conservation of the structure of the apparently inactive D1 may be related to constraints imposed by structural changes that could potentially impact substrate binding in D2 and/or possibly influence the proper folding of the enzyme during synthesis. Overall, the results from the present study indicate that the AK contiguous dimer from Ensis directus functions with activity in only the second domain. Although lacking activity in D1, D2 appears to compensate by having a higher intrinsic catalytic throughput than typical 40-kDa monomeric AKs.
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Affiliation(s)
- Deanne M Compaan
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4370, USA
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Cox JM, Davis CA, Chan C, Jourden MJ, Jorjorian AD, Brym MJ, Snider MJ, Borders CL, Edmiston PL. Generation of an active monomer of rabbit muscle creatine kinase by site-directed mutagenesis: the effect of quaternary structure on catalysis and stability. Biochemistry 2003; 42:1863-71. [PMID: 12590573 DOI: 10.1021/bi027083b] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytosolic creatine kinase exists in native form as a dimer; however, the reasons for this quaternary structure are unclear, given that there is no evidence of active site communication and more primitive guanidino kinases are monomers. Three fully conserved residues found in one-half of the dimer interface of the rabbit muscle creatine kinase (rmCK) were selectively changed to alanine by site-directed mutagenesis. Four mutants were prepared, overexpressed, and purified: R147A, R151A, D209A, and R147A/R151A. Both the R147A and R147A/R151A were confirmed by size-exclusion chromatography and analytical ultracentrifugation to be monomers, whereas R151A was dimeric and D209A appeared to be an equilibrium mixture of dimers and monomers. Kinetic analysis showed that the monomeric mutants, R147A and R147A/R151A, showed substantial enzymatic activity. Substrate binding affinity by R147A/R151A was reduced approximately 10-fold, although k(cat) was 60% of the wild-type enzyme. Unlike the R147A/R151A, the kinetic data for the R147A mutant could not be fit to a random-order rapid-equilibrium mechanism characteristic of the wild-type, but could only be fit to an ordered mechanism with creatine binding first. Substrate binding affinities were also significantly lower for the R147A mutant, but k(cat) was 11% that of the native enzyme. Fluorescence measurements using 1-anilinonaphthalene-8-sufonate showed that increased amounts of hydrophobic surface area are exposed in all of the mutants, with the monomeric mutants having the greatest amounts of unfolding. Thermal inactivation profiles demonstrated that protein stability is significantly decreased in the monomeric mutants compared to wild-type. Denaturation experiments measuring lambda(max) of the intrinsic fluorescence as a function of guanidine hydrochloride concentration helped confirm the quaternary structures and indicated that the general unfolding pathway of all the mutants are similar to that of the wild-type. Collectively, the data show that dimerization is not a prerequisite for activity, but there is loss of structure and stability upon formation of a CK monomer.
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Affiliation(s)
- Julia M Cox
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, USA
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Suzuki T, Tomoyuki T, Uda K. Kinetic properties and structural characteristics of an unusual two-domain arginine kinase of the clam Corbicula japonica. FEBS Lett 2003; 533:95-8. [PMID: 12505165 DOI: 10.1016/s0014-5793(02)03765-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Arginine kinase (AK) from the clam Corbicula japonica is a unique enzyme in that it has an unusual two-domain structure with molecular mass of 80 kDa. It lacks two functionally important amino acid residues, Asp-62 and Arg-193, which are conserved in other 40 kDa AKs and are assumed to be key residues for stabilizing the substrate-bound structure. K m arg and Vmax values for the recombinant two-domain AK were determined. These values were close to those of usual 40 kDa AKs, although Corbicula AK lacks the functionally important Asp-62 and Arg-193. Domain 2 of Corbicula AK was separated from the two-domain enzyme and was expressed in Escherichia coli. Domain 2 still exhibited activity. However, kinetic parameters for domain 2 appeared to be slightly, but significantly, different from those of two-domain AK. Thus, it is likely that the formation of the contiguous dimer alters the kinetic properties of its constituent domains significantly. Comparison of K d arg and K m arg for two-domain AK and its domain 2 showed that the affinity of the enzyme for arginine is greater in the presence of substrate ATP than in its absence. Presumably this difference is correlated with the large structural differences in the enzyme in the presence or absence of substrate, namely open and closed structures. We expressed three mutants of Corbicula AK domain 2 (His-60 to Gly or Arg, Asp-197 to Gly), and determined their K m arg and Vmax values. The affinity for the substrate arginine in mutant enzymes was reduced considerably, accompanied by a decrease in Vmax. These results suggest that His-60 and Asp-197 affect the substrate binding system, and are consistent with the hypothesis that a hydrogen bond is formed between His-60 and Asp-197 in Corbicula AK as a substitute for the Asp-62 and Arg-193 bond in normal AKs.
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Affiliation(s)
- Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, 780-8520, Kochi, Japan.
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Suzuki T, Sugimura N, Taniguchi T, Unemi Y, Murata T, Hayashida M, Yokouchi K, Uda K, Furukohri T. Two-domain arginine kinases from the clams Solen strictus and Corbicula japonica: exceptional amino acid replacement of the functionally important D(62) by G. Int J Biochem Cell Biol 2002; 34:1221-9. [PMID: 12127572 DOI: 10.1016/s1357-2725(02)00050-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Arginine kinases (AKs) isolated from the adductor muscle of the clams Solen strictus and Corbicula japonica have relative molecular masses of 80 kDa as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in contrast to the 40 kDa AKs found in Mollusca and Arthropoda. The cDNAs encoding Solen and Corbicula AKs have open reading frames of 2175 nucleotides (724 amino acid protein) and 2172 nucleotides (723 amino acid protein), respectively. The amino acid sequence clearly indicates that Solen and Corbicula AKs have a two-domain structure: the first-domain includes residues 1-363 and the second-domain includes residue 364 to the end. There is approximately 60% inter-domain amino acid identity. It is clear that gene-duplication and subsequent fusion occurred in the immediate ancestor of the clams Solen, Corbicula, and Pseudocardium. During substrate binding, it is proposed that AK undergoes a substrate-induced conformational change and that the hydrogen bond between D(62) and R(193) stabilizes the substrate-bound structure. However, in Solen and Corbicula two-domain AKs, D(62) is replaced by a G, and R(193) by A, S, or D. Consequently, the two-domain AKs can not form the stabilizing hydrogen bond. Nevertheless, the enzyme activity of Corbicula AK is comparable to those of other molluscan 40 kDa AKs. We assumed that the substrate-bound structure of the two-domain AK is stabilized not by the hydrogen bond between D(62) and R(193) but by the bond between H(60) and D(197), characteristic of the unusual two-domain AKs. This explains why D(62) and R(193), which remain highly conserved in other AKs, have undergone amino acid replacements in Solen and Corbicula AKs.
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Affiliation(s)
- Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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43
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Graber NA, Ellington WR. Gene duplication events producing muscle (M) and brain (B) isoforms of cytoplasmic creatine kinase: cDNA and deduced amino acid sequences from two lower chordates. Mol Biol Evol 2001; 18:1305-14. [PMID: 11420369 DOI: 10.1093/oxfordjournals.molbev.a003915] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Creatine kinase (CK) is coded for by at least four loci in higher vertebrates--two cytoplasmic isoforms, muscle (M) and brain (B), and two mitochondrial isoforms, sarcomeric and ubiquitous. M is expressed primarily in skeletal muscle, while B is expressed in a variety of cells, including cardiac and smooth muscle fibers, neurons, transport epithelia, and photoreceptors. M and B subunits form very stable homodimers (MM [M-CK], BB [B-CK]) and heterodimers (MB). M-CK is capable of binding to the M line of the myofibril, thereby creating an energy transfer microcompartment; BB and MB CKs are not. M- and B-like CKs are present in all vertebrates yet examined, including fish. Cytoplasmic, dimeric CKs are widely distributed in the invertebrates. The only available amino acid sequence for an invertebrate dimeric CK, that of the protostome polychaete Chaetopterus variopedatus, is just as similar to the vertebrate M isoform as to the B isoform. Echinoderms lack dimeric, cytoplasmic CKs, which appear to be replaced by a dimeric arginine kinase which evolved secondarily from CK. Thus, it is likely that the gene duplication event producing the M and B isoforms occurred after the divergence of the chordates from echinoderms. To narrow down the timing of this duplication event, we obtained the cDNA and deduced amino acid sequences of dimeric CKs from the tunicate Ciona intestinalis (subphylum Urochordata) and the lancelet Branchiostoma floridae (subphylum Cephalochordata). Our results show that these CKs are strikingly similar to both invertebrate and vertebrate CKs. However, phylogenetic analyses by neighbor-joining and parsimony show that these two enzymes appeared to have diverged before the point of divergence of the M and B isoforms. Thus, the gene duplication event for formation of the muscle and brain isoforms of CK most likely occurred during the radiation of the fish, a time noted for gene duplication events at a variety of other loci.
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Affiliation(s)
- N A Graber
- Institute of Molecular Biophysics and Department of Biological Science, Florida State University, Tallahassee, 32306-4370, USA
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Edmiston PL, Schavolt KL, Kersteen EA, Moore NR, Borders CL. Creatine kinase: a role for arginine-95 in creatine binding and active site organization. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1546:291-8. [PMID: 11295435 DOI: 10.1016/s0167-4838(01)00159-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sequence homology analysis reveals that arginine-95 is fully conserved in 29 creatine kinases sequenced to date, but fully conserved as a tyrosine residue in 16 arginine kinases. Site-directed mutants of rabbit muscle creatine kinase (rmCK) were prepared in which R95 was replaced by a tyrosine (R95Y), alanine (R95A), or lysine (R95K). Kinetic analysis of phosphocreatine formation for each purified mutant showed that recombinant native rmCK and all R95 mutants follow a random-order, rapid-equilibrium mechanism. However, we observed no evidence for synergism of substrate binding by the recombinant native enzyme, as reported previously [Maggio et al., (1977) J. Biol. Chem. 252, 1202-1207] for creatine kinase isolated directly from rabbit muscle. The catalytic efficiencies of R95Y and R95A are reduced approximately 3000- and 2000-fold, respectively, compared to native enzyme, but that of R95K is reduced only 30-fold. The major contribution to the reduction of the catalytic efficiency of R95K is a 5-fold reduction in the affinity for creatine. This suggests that while a basic residue is required at position 95 for optimal activity, R95 is not absolutely essential for binding or catalysis in CK. R95Y has a significantly lower affinity for creatine than the native enzyme, but it also displays a somewhat lower affinity for MgATP and 100-fold reduction in k(cat). Interestingly, R95A appears to bind either creatine or MgATP first with affinities similar to those for the native enzyme, but it has a 10-fold lower affinity for the second substrate, suggesting that replacement of R95 by an alanine disrupts the active site organization and reduces the efficiency of formation of the catalytically competent ternary complex.
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Affiliation(s)
- P L Edmiston
- Department of Chemistry, College of Wooster, 44691, Wooster, OH, USA
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45
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Pineda AO, Ellington WR. Organization of the gene for an invertebrate mitochondrial creatine kinase: comparisons with genes of higher forms and correlation of exon boundaries with functional domains. Gene 2001; 265:115-21. [PMID: 11255014 DOI: 10.1016/s0378-1119(01)00352-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Two major gene duplication events are thought to have taken place in the evolution of creatine kinases (CK) in the vertebrates - (1) the formation of distinct mitochondrial (MiCK) and cytoplasmic forms from the primordial gene and (2) subsequent formation of the sarcomeric (sar-) and ubiquitous (ubi-) isoforms of octameric MiCK and muscle (M) and brain (B) isoforms of dimeric, cytoplasmic CK. The genes of these two CK clades reflect a distant divergence as sar- and ubiMiCK genes consistently have nine protein-coding exons while M- and B-CK genes have seven protein-coding exons; these genes share only one common exon. CKs are also widely distributed in the invertebrates and it has recently been shown that MiCKs evolved well before the divergence of the major metazoan groups. In the present communication, we report the structure and topology of the gene for MiCK from the protostome marine worm Chaetopterus variopedatus. The protein-coding region of the gene for this primitive MiCK spans over 10 kb and consists of eight exons, the last five (E4-E8) have identical boundaries to the corresponding exons of sar- and ubiMiCK genes. Exon-3 of the C. variopedatus MiCK gene consists of the corresponding E3 and E4 of the vertebrate MiCKs with no intervening intron. E1 is longer and E2 is shorter in the polychaete MiCK gene than the counterpart sarcomeric and ubiquitous genes. The insertion of the intron in C. variopedatus E3 creating the two exons as well as the rearrangement of the intron between E1 and E2 must have occurred prior to or coincident with the duplication event creating the two vertebrate mitochondrial isoforms. Sarcomeric and ubiMiCKs display substantial differences from their invertebrate MiCK counterparts in properties relating to octamer stability and membrane binding. The evolutionary changes in gene topology may be a component of this functional progression.
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Affiliation(s)
- A O Pineda
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, 32306-4370, Tallahassee, FL, USA
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Suzuki T, Yamamoto Y. Gene structure of two-domain arginine kinases from Anthopleura japonicus and Pseudocardium sachalinensis. Comp Biochem Physiol B Biochem Mol Biol 2000; 127:513-8. [PMID: 11281268 DOI: 10.1016/s0305-0491(00)00281-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Unusual two-domain arginine kinases (AKs) arose independently at least two times during molecular evolution of phosphagen kinases: AKs from the primitive sea anemone Anthopleurura japonicus and from the clam Pseudocardium sachalinensis. To elucidate its unusual evolution, the structures of Anthopleura and Pseudocardium AK genes have been determined. The Anthopleura gene consisted of 4 exons and 3 introns: two domains are linked by a bridge intron, and each domain contains one intron in different positions. On the other hand, the Pseudocardium gene consisted of 10 exons and 9 introns: two domains are also linked by a bridge intron, and domains 1 and 2 contains 3 and 5 introns, respectively, of which 3 introns are located in exactly same positions. Since the two domains of Pseudocardium AK are estimated to have diverged about 290 million years ago, the 3 introns have been conserved at least for this long. Comparison of intron positions in Anthopleura, Pseudocardium and C. elegans AK genes indicates that there is no intron conserved through the three AK lineages, in sharp contrast to relatively conservative intron positions in creatine kinase (CK) gene family.
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Affiliation(s)
- T Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Japan.
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Suzuki T, Inoue N, Higashi T, Mizobuchi R, Sugimura N, Yokouchi K, Furukohri T. Gastropod arginine kinases from Cellana grata and Aplysia kurodai. Isolation and cDNA-derived amino acid sequences. Comp Biochem Physiol B Biochem Mol Biol 2000; 127:505-12. [PMID: 11281267 DOI: 10.1016/s0305-0491(00)00280-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Arginine kinase (AK) was isolated from the radular muscle of the gastropod molluscs Cellana grata (subclass Prosobranchia) and Aplysia kurodai (subclass Opisthobranchia), respectively, by ammonium sulfate fractionation, Sephadex G-75 gel filtration and DEAE-ion exchange chromatography. The denatured relative molecular mass values were estimated to be 40 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The isolated enzyme from Aplysia gave a Km value of 0.6 mM for arginine and a Vmax value of 13 micromole Pi min(-1) mg protein(-1) for the forward reaction. These values are comparable to other molluscan AKs. The cDNAs encoding Cellana and Aplysia AKs were amplified by polymerase chain reaction, and the nucleotide sequences of 1,608 and 1,239 bp, respectively, were determined. The open reading frame for Cellana AK is 1044 nucleotides in length and encodes a protein with 347 amino acid residues, and that for A. kurodai is 1077 nucleotides and 354 residues. The cDNA-derived amino acid sequences were validated by chemical sequencing of internal lysyl endopeptidase peptides. The amino acid sequences of Cellana and Aplysia AKs showed the highest percent identity (66-73%) with those of the abalone Nordotis and turbanshell Battilus belonging to the same class Gastropoda. These AK sequences still have a strong homology (63-71%) with that of the chiton Liolophura (class Polyplacophora), which is believed to be one of the most primitive molluscs. On the other hand, these AK sequences are less homologous (55-57%) with that of the clam Pseudocardium (class Bivalvia), suggesting that the biological position of the class Polyplacophora should be reconsidered.
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Affiliation(s)
- T Suzuki
- Department of Biology, Faculty of Science, Kochi University, Japan.
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Suzuki T, Fukuta H, Nagato H, Umekawa M. Arginine kinase from Nautilus pompilius, a living fossil. Site-directed mutagenesis studies on the role of amino acid residues in the Guanidino specificity region. J Biol Chem 2000; 275:23884-90. [PMID: 10811656 DOI: 10.1074/jbc.m002926200] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arginine kinases were isolated from the cephalopods Nautilus pompilius, Octopus vulgaris, and Sepioteuthis lessoniana, and the cDNA-derived amino acid sequences have been determined. Although the origin and evolution of cephalopods have long been obscure, this work provides the first molecular evidence for the phylogenetic position of Cephalopoda in molluscan evolution. A crystal structure for Limulus arginine kinase showed that four amino acid residues (Ser(63), Gly(64), Val(65), and Tyr(68)) are hydrogen-bonded with the substrate arginine. We introduced three independent mutations, Ser(63) --> Gly, Ser(63) --> Thr, and Tyr(68) --> Ser, in Nautilus arginine kinase. One of the mutants had a considerably reduced substrate affinity, accompanied by a decreased V(max). In other mutants, the activity was lost almost completely. It is known that substantial conformational changes take place upon substrate binding in arginine kinase. We hypothesize that the hydrogen bond between Asp(62) and Arg(193) stabilizes the closed, substrate-bound state. Site-directed mutagenesis studies strongly support this hypothesis. The mutant (Asp(62) --> Gly or Arg(193) --> Gly), which destabilizes the maintenance of the closed state and/or perhaps disrupts the unique topology of the catalytic pocket, showed only a very weak activity (0.6-1.5% to the wild-type).
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Affiliation(s)
- T Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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