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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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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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Wang Z, Qiao Z, Ye S, Zhang R. Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains. ACTA ACUST UNITED AC 2015; 71:779-89. [PMID: 25849389 DOI: 10.1107/s1399004715001169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/20/2015] [Indexed: 12/27/2022]
Abstract
Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.
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Affiliation(s)
- Zhiming Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Zhu Qiao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Sheng Ye
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Rongguang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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Shi X, Wang L, Zhou Z, Yang C, Gao Y, Wang L, Song L. The arginine kinase in Zhikong scallop Chlamys farreri is involved in immunomodulation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 37:270-278. [PMID: 22480717 DOI: 10.1016/j.dci.2012.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/14/2012] [Accepted: 03/15/2012] [Indexed: 05/31/2023]
Abstract
Arginine kinase (AK) catalyzes the reversible phosphorylation of l-arginine to form phosphoarginine, and plays a critical role in energy metabolism in invertebrates. In the present study, a scallop AK gene was identified from Chlamys farreri with an open reading frame (ORF) of 1101bp encoding for a protein of 366 amino acids (designed as CfAK). An ATP-gua PtransN domain which was described as a guanidine substrate specificity domain (GS domain) and an ATP-gua Ptrans domian which was responsible for binding ATP, were both identified in CfAK. The mRNA transcripts of CfAK were detectable in haemocytes, hepatopancreas, adductor muscle, mantle, gill, kidney and gonad, with the highest expression level in the muscle and the lowest level in the hemocytes. The expression level of CfAK mRNA increased from fertilized eggs to eyebot, and reached the highest in the trochophore stage. The relative expression level of CfAK mRNA in muscle was up-regulated significantly after LPS (0.5mg/mL) stimulation, and reached the peak at 6h (5.2-fold, P<0.05). The activity of inducible nitric oxide synthase (iNOS) in the supernatant of muscle homogenate increased significantly from 3.2U/mg at 0 h to 9.7 U/mg at 12h after LPS stimulation, while the concentration of nitric oxide (NO) in the supernatant of muscle homogenate began to increase at 3h (21.55 μmol/L), and reached the top concentration at 24h (42.27 μmol/L), then recovered to the normal level after 48 h. The recombinant protein of CfAK (rCfAK) expressed in Escherichia coli displayed Arginine kinase activity, and its apparent K(m) was 0.82 ± 0.11 and 1.24 ± 0.13 mM for L-arginine and ATP-Na, respectively. The results indicated that the CfAK was involved in energy production and utilization during the whole life process, and might refer to the immunomodulation process via altering the NO concentration and iNOS activity in scallop Chlamys farreri.
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Affiliation(s)
- Xiaowei Shi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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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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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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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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Wang JS, Zheng ZL, Lei J, Pan JC, Zou GL. Cloning, expression, characterization and phylogenetic analysis of arginine kinase from greasyback shrimp (Metapenaeus ensis). Comp Biochem Physiol B Biochem Mol Biol 2009; 153:268-74. [PMID: 19341812 DOI: 10.1016/j.cbpb.2009.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Revised: 03/17/2009] [Accepted: 03/18/2009] [Indexed: 11/28/2022]
Abstract
Arginine kinase (AK) plays an important role in cellular energy metabolism in invertebrate. The encoding AK gene from Shrimp Metapenaeus ensis (M. ensis) was cloned in prokaryotic expression plasmid pET-28a, and it was then expressed in Escherichia coil in dissoluble form. The recombinant protein was purified by following three chromatography steps in turn: CM-Cellulose cation-exchange, Sephacryl S-100HR gel filtrate and DEAE-Sepharose anion-exchange. The purified AK's apparent K(m) was 2.33+/-0.1 and 1.59+/-0.2 mM for ATP and l-arginine, respectively, while its optimum pH and temperature was 8.5 and 30 degrees C in the process of forward reaction, respectively. Phylogenetic analysis of cDNA-derived amino acid sequences for the AKs indicated a close affinity of M. ensis and another shrimp (Litopenaeus vannamei).
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Affiliation(s)
- Jin-Song Wang
- State Key Laboratory of Virology, College of Life Sciences, Center of Nanoscience and Nanotechnology, Wuhan University, Wuhan, Hubei 430072, PR China
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Uda K, Kuwasaki A, Shima K, Matsumoto T, Suzuki T. The role of Arg-96 in Danio rerio creatine kinase in substrate recognition and active center configuration. Int J Biol Macromol 2009; 44:413-8. [PMID: 19428475 DOI: 10.1016/j.ijbiomac.2009.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2008] [Revised: 02/19/2009] [Accepted: 03/02/2009] [Indexed: 11/30/2022]
Abstract
In creatine kinases (CKs), the amino acid residue-96 is a strictly conserved arginine. This residue is not directly associated with substrate binding, but it is located close to the binding site of the substrate creatine. On the other hand, the residue-96 is known to be involved in expression in the substrate specificity of various other phosphagen (guanidino) kinases, since each enzyme has a specific residue at this position: arginine kinase (Tyr), glycocyamine kinase (Ile), taurocyamine kinase (His) and lombricine kinase (Lys). To gain a greater understanding of the role of residue-96 in CKs, we replaced this residue in zebra fish Danio rerio cytoplasmic CK with other 19 amino acids, and expressed these constructs in Escherichia coli. All the twenty recombinant enzymes, including the wild-type, were obtained as soluble form, and their activities were determined in the forward direction. Compared with the activity of wild-type, the R96K mutant showed significant activity (8.3% to the wild-type), but 10 mutants (R96Y, A, S, E, H, T, F, C, V and N) showed a weak activity (0.056-1.0%). In the remaining mutants (R96Q, G, M, P, L, W, D and I), the activity was less than 0.05%. Our mutagenesis studies indicated that Arg-96 in Danio CK can be substituted for partially by Lys, but other replacements caused remarkable loss of activity. From careful inspection of the crystal structures (transition state analog complex (TSAC) and open state) of Torpedo cytoplasmic CK, we found that the side chain of R96 forms hydrogen bonds with A339 and D340 only in the TSAC structure. Based on the assumption that CKs consist of four dynamic domains (domains 1-3, and fixed domain), the above hydrogen bonds act to link putative domains 1 and 3 in TSAC structure. We suggest that residue-96 in CK and equivalent residues in other phosphagen kinases, which are structurally similar, have dual roles: (1) one involves in distinguishing guanidino substrates, and (2) the other plays a key role in organizing the hydrogen-bond network around residue-96 which offers an appropriate active center for the high catalytic turnover. The mode of development of the network appears to be unique each phosphagen kinase, reflecting evolution of each enzyme.
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Affiliation(s)
- Kouji Uda
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
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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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Characterization of a novel bacterial arginine kinase from Desulfotalea psychrophila. Comp Biochem Physiol B Biochem Mol Biol 2008; 150:312-9. [PMID: 18499493 DOI: 10.1016/j.cbpb.2008.03.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 03/30/2008] [Accepted: 03/31/2008] [Indexed: 11/22/2022]
Abstract
Phosphagen kinases are found throughout the animal kingdom and catalyze the transfer of a high-energy gamma phosphoryl-group from ATP to a guanidino group on a suitable acceptor molecule such as creatine or arginine. Recent genome sequencing efforts in several proteobacteria, including Desulfotalea psychrophila LSv54, Myxococcus xanthus, Sulfurovum sp. NBC37-1, and Moritella sp. PE36 have revealed what appears to be a phosphagen kinase homolog present in their genomes. Based on sequence comparisons these putative homologs bear a strong resemblance to arginine kinases found in many invertebrates and some protozoa. We describe here a biochemical characterization of one of these homologs from D. psychrophila expressed in E. coli that confirms its ability to reversibly catalyze phosphoryl transfer from ATP to arginine. A phylogenetic analysis suggests that these bacteria homologs are not widely distributed in proteobacteria species. They appear more related to protozoan arginine kinases than to similar proteins seen in some Gram-positive bacteria that share key catalytic residues but encode protein tyrosine kinases. This raises the possibility of horizontal gene transfer as a likely origin of the bacterial arginine kinases.
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