1
|
Pcal_0976, a pullulanase homologue from Pyrobaculum calidifontis, displays a glycoside hydrolase activity but no pullulanase activity. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-022-01309-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
2
|
Lahham M, Jha S, Goj D, Macheroux P, Wallner S. The family of sarcosine oxidases: Same reaction, different products. Arch Biochem Biophys 2021; 704:108868. [PMID: 33812916 DOI: 10.1016/j.abb.2021.108868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022]
Abstract
The subfamily of sarcosine oxidase is a set of enzymes within the larger family of amine oxidases. It is ubiquitously distributed among different kingdoms of life. The member enzymes catalyze the oxidization of an N-methyl amine bond of amino acids to yield unstable imine species that undergo subsequent spontaneous non-enzymatic reactions, forming an array of different products. These products range from demethylated simple species to complex alkaloids. The enzymes belonging to the sarcosine oxidase family, namely, monomeric and heterotetrameric sarcosine oxidase, l-pipecolate oxidase, N-methyltryptophan oxidase, NikD, l-proline dehydrogenase, FsqB, fructosamine oxidase and saccharopine oxidase have unique features differentiating them from other amine oxidases. This review highlights the key attributes of the sarcosine oxidase family enzymes, in terms of their substrate binding motif, type of oxidation reaction mediated and FAD regeneration, to define the boundaries of this group and demarcate these enzymes from other amine oxidase families.
Collapse
Affiliation(s)
- Majd Lahham
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria; Department of Biochemistry and Microbiology, Aljazeera Private University, Ghabagheb, Syria
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Dominic Goj
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria.
| |
Collapse
|
3
|
Satomura T, Hayashi J, Sakamoto H, Nunoura T, Takaki Y, Takai K, Takami H, Ohshima T, Sakuraba H, Suye SI. d-Lactate electrochemical biosensor prepared by immobilization of thermostable dye-linked d-lactate dehydrogenase from Candidatus Caldiarchaeum subterraneum. J Biosci Bioeng 2018; 126:425-430. [PMID: 29691195 DOI: 10.1016/j.jbiosc.2018.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 11/30/2022]
Abstract
A stable d-lactate electrochemical sensing system was developed using a dye-linked d-lactate dehydrogenase (Dye-DLDH) from an uncultivated thermophilic archaeon, Candidatus Caldiarchaeum subterraneum. To develop the system, the putative gene encoding the Dye-DLDH from Ca. Caldiarchaeum subterraneum was overexpressed in Escherichia coli, and the expressed product was purified. The recombinant enzyme was a highly thermostable Dye-DLDH that retained full activity after incubation for 10 min at 70°C. The electrode for detection of d-lactate was prepared by immobilizing the thermostable Dye-DLDH and multi-walled carbon nanotube (MWCNT) within Nafion membrane. The electrocatalytic response of the electrode was clearly observed upon exposure to d-lactate. The electrode response to d-lactate was linear within the concentration range of 0.03-2.5 mM, and it showed little reduction in responsiveness after 50 days. This is the first report describing a d-lactate sensing system using a thermostable Dye-DLDH.
Collapse
Affiliation(s)
- Takenori Satomura
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan.
| | - Junji Hayashi
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Hiroaki Sakamoto
- Tenure-Track Program for Innovative Research, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| | - Takuro Nunoura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hideto Takami
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technoligy, Ohmiya, 5-16-1 Asahi-ku, Ohsaka 535-8585 Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Shin-Ichiro Suye
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| |
Collapse
|
4
|
Watanabe S, Morimoto D, Fukumori F, Watanabe Y. Characterization of cis-4-hydroxy-D-proline dehydrogenase from Sinorhizobium meliloti. Biosci Biotechnol Biochem 2017; 82:110-113. [PMID: 29191113 DOI: 10.1080/09168451.2017.1403887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The hypO gene from Sinorhizobium meliloti, located within the trans-4-hydroxy-L-proline metabolic gene cluster, was first successfully expressed in the host Pseudomonas putida. Purified HypO protein functioned as a FAD-containing cis-4-hydroxy-D-proline dehydrogenase with a homomeric structure. In contrast to other known enzymes, significant activity for D-proline was found, confirming a previously proposed potential involvement in D-proline metabolism.
Collapse
Affiliation(s)
- Seiya Watanabe
- a Department of Bioscience, Graduate School of Agriculture , Ehime University , Matsuyama , Japan.,b Faculty of Agriculture , Ehime University , Matsuyama , Japan.,c Center for Marine Environmental Studies , Ehime University , Matsuyama , Japan
| | - Daichi Morimoto
- b Faculty of Agriculture , Ehime University , Matsuyama , Japan.,e Graduate School of Agriculture , Kyoto University , Kyoto , Japan
| | - Fumiyasu Fukumori
- d Faculty of Food and Nutritional Sciences , Toyo University , Gunma , Japan
| | - Yasuo Watanabe
- a Department of Bioscience, Graduate School of Agriculture , Ehime University , Matsuyama , Japan.,b Faculty of Agriculture , Ehime University , Matsuyama , Japan
| |
Collapse
|
5
|
Hayashi J, Yamamoto K, Yoneda K, Ohshima T, Sakuraba H. Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis. Proteins 2016; 84:1786-1796. [PMID: 27616573 DOI: 10.1002/prot.25161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/08/2016] [Accepted: 09/02/2016] [Indexed: 11/08/2022]
Abstract
A gene encoding an sn-glycerol-1-phosphate dehydrogenase (G1PDH) was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The gene was overexpressed in Escherichia coli, and its product was purified and characterized. In contrast to conventional G1PDHs, the expressed enzyme showed strong preference for NADH: the reaction rate (Vmax ) with NADPH was only 2.4% of that with NADH. The crystal structure of the enzyme was determined at a resolution of 2.45 Å. The asymmetric unit consisted of one homohexamer. Refinement of the structure and HPLC analysis showed the presence of the bound cofactor NADPH in subunits D, E, and F, even though it was not added in the crystallization procedure. The phosphate group at C2' of the adenine ribose of NADPH is tightly held through the five biased hydrogen bonds with Ser40 and Thr42. In comparison with the known G1PDH structure, the NADPH molecule was observed to be pushed away from the normal coenzyme binding site. Interestingly, the S40A/T42A double mutant enzyme acquired much higher reactivity than the wild-type enzyme with NADPH, which suggests that the biased interactions around the C2'-phosphate group make NADPH binding insufficient for catalysis. Our results provide a unique structural basis for coenzyme preference in NAD(P)-dependent dehydrogenases. Proteins 2016; 84:1786-1796. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Junji Hayashi
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan
| | - Kaori Yamamoto
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan
| | - Kazunari Yoneda
- Department of Bioscience, School of Agriculture, Tokai University, Aso, Kumamoto, 869-1404, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka, 535-8585, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan
| |
Collapse
|
6
|
Watanabe S, Hiraoka Y, Endo S, Tanimoto Y, Tozawa Y, Watanabe Y. An enzymatic method to estimate the content of L-hydroxyproline. J Biotechnol 2015; 199:9-16. [DOI: 10.1016/j.jbiotec.2015.01.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 01/27/2015] [Accepted: 01/31/2015] [Indexed: 11/27/2022]
|
7
|
Molecular Cloning and Expression Analysis of the Gene Encoding Proline Dehydrogenase from Jatropha curcas L. Appl Biochem Biotechnol 2014; 175:2413-26. [PMID: 25502926 DOI: 10.1007/s12010-014-1441-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 12/01/2014] [Indexed: 10/24/2022]
|
8
|
Gene Expression and Characterization of a Third Type of Dye-LinkedL-Proline Dehydrogenase from the Aerobic Hyperthermophilic Archaeon,Aeropyrum pernix. Biosci Biotechnol Biochem 2014; 76:589-93. [DOI: 10.1271/bbb.110775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
9
|
Watanabe S, Morimoto D, Fukumori F, Shinomiya H, Nishiwaki H, Kawano-Kawada M, Sasai Y, Tozawa Y, Watanabe Y. Identification and characterization of D-hydroxyproline dehydrogenase and Delta1-pyrroline-4-hydroxy-2-carboxylate deaminase involved in novel L-hydroxyproline metabolism of bacteria: metabolic convergent evolution. J Biol Chem 2012; 287:32674-88. [PMID: 22833679 DOI: 10.1074/jbc.m112.374272] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
L-hydroxyproline (4-hydroxyproline) mainly exists in collagen, and most bacteria cannot metabolize this hydroxyamino acid. Pseudomonas putida and Pseudomonas aeruginosa convert L-hydroxyproline to α-ketoglutarate via four hypothetical enzymatic steps different from known mammalian pathways, but the molecular background is rather unclear. Here, we identified and characterized for the first time two novel enzymes, D-hydroxyproline dehydrogenase and Δ(1)-pyrroline-4-hydroxy-2-carboxylate (Pyr4H2C) deaminase, involved in this hypothetical pathway. These genes were clustered together with genes encoding other catalytic enzymes on the bacterial genomes. D-hydroxyproline dehydrogenases from P. putida and P. aeruginosa were completely different from known bacterial proline dehydrogenases and showed similar high specificity for substrate (D-hydroxyproline) and some artificial electron acceptor(s). On the other hand, the former is a homomeric enzyme only containing FAD as a prosthetic group, whereas the latter is a novel heterododecameric structure consisting of three different subunits (α(4)β(4)γ(4)), and two FADs, FMN, and [2Fe-2S] iron-sulfur cluster were contained in αβγ of the heterotrimeric unit. These results suggested that the L-hydroxyproline pathway clearly evolved convergently in P. putida and P. aeruginosa. Pyr4H2C deaminase is a unique member of the dihydrodipicolinate synthase/N-acetylneuraminate lyase protein family, and its activity was competitively inhibited by pyruvate, a common substrate for other dihydrodipicolinate synthase/N-acetylneuraminate lyase proteins. Furthermore, disruption of Pyr4H2C deaminase genes led to loss of growth on L-hydroxyproline (as well as D-hydroxyproline) but not L- and D-proline, indicating that this pathway is related only to L-hydroxyproline degradation, which is not linked to proline metabolism.
Collapse
Affiliation(s)
- Seiya Watanabe
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Kawakami R, Noguchi C, Higashi M, Sakuraba H, Ohshima T. Comparative analysis of the catalytic components in the archaeal dye-linked L-proline dehydrogenase complexes. Appl Microbiol Biotechnol 2012; 97:3419-27. [PMID: 22752365 DOI: 10.1007/s00253-012-4201-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 05/11/2012] [Accepted: 05/15/2012] [Indexed: 11/24/2022]
Abstract
Two types of hetero-oligomeric dye-linked L-proline dehydrogenases (α4β4 and αβγδ types) are expressed in the hyperthermophilic archaea belonging to Thermococcales. In both enzymes, the β subunit (PDHβ) is responsible for catalyzing L-proline dehydrogenation. The genes encoding the two enzyme types form respective clusters that are completely conserved among Pyrococcus and Thermococcus strains. To compare the enzymatic properties of PDHβs from α4β4- and αβγδ-type enzyme complexes, eight PDHβs (four of each type) from Pyrococcus furiosus DSM3638, Pyrococcus horikoshii OT-3, Thermococcus kodakaraensis KOD1 JCM12380 and Thermococcus profundus DSM9503 were expressed in Escherichia coli cells and purified to homogeneity using one-step Ni-chelating chromatography. The α4β4-type PDHβs showed greater thermostability than most of the αβγδ-type PDHβs: the former retained more than 80 % of their activity after heating at 70 °C for 20 min, while the latter showed different thermostabilities under the same conditions. In addition, the α4β4-type PDHβs utilized ferricyanide as the most preferable electron acceptor, whereas αβγδ-type PDHβs preferred 2, 6-dichloroindophenol, with one exception. These results indicate that the differences in the enzymatic properties of the PDHβs likely reflect whether they were from an αβγδ- or α4β4-type complex, though the wider divergence observed within αβγδ-type PDHβs based on the phylogenetic analysis may also be responsible for their inconsistent enzymatic properties. By contrast, differences in the kinetic parameters among the PDHβs did not reflect the complex type. Interestingly, the k cat value for free α4β4-type PDHβ from P. horikoshii was much larger than the value for the same subunit within the α4β4-complex. This indicates that the isolated PDHβ could be a useful element for an electrochemical system for detection of L-proline.
Collapse
Affiliation(s)
- Ryushi Kawakami
- Analytical Research Center for Experimental Sciences, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | | | | | | | | |
Collapse
|
11
|
Sakuraba H, Satomura T, Kawakami R, Kim K, Hara Y, Yoneda K, Ohshima T. Crystal structure of novel dye-linked L-proline dehydrogenase from hyperthermophilic archaeon Aeropyrum pernix. J Biol Chem 2012; 287:20070-80. [PMID: 22511758 DOI: 10.1074/jbc.m111.319038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two types of dye-linked L-proline dehydrogenase (PDH1, α4β4-type hetero-octamer, and PDH2, αβγδ-type heterotetramer) have been identified so far in hyperthermophilic archaea. Here, we report the crystal structure of a third type of L-proline dehydrogenase, found in the aerobic hyperthermophilic archaeon Aeropyrum pernix, whose structure (homodimer) is much simpler than those of previously studied L-proline dehydrogenases. The structure was determined at a resolution of 1.92 Å. The asymmetric unit contained one subunit, and a crystallographic 2-fold axis generated the functional dimer. The overall fold of the subunit showed similarity to that of the PDH1 β-subunit, which is responsible for catalyzing L-proline dehydrogenation. However, the situation at the subunit-subunit interface of the A. pernix enzyme was totally different from that in PDH1. The presence of additional surface elements in the A. pernix enzyme contributes to a unique dimer association. Moreover, the C-terminal Leu(428), which is provided by a tail extending from the FAD-binding domain, shielded the active site, and an L-proline molecule was entrapped within the active site cavity. The K(m) value of a Leu(428) deletion mutant for L-proline was about 800 times larger than the K(m) value of the wild-type enzyme, although the k(cat) values did not differ much between the two enzymes. This suggests the C-terminal Leu(428) is not directly involved in catalysis, but it is essential for maintaining a high affinity for the substrate. This is the first description of an LPDH structure with L-proline bound, and it provides new insight into the substrate binding of LPDH.
Collapse
Affiliation(s)
- Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | | | | | | | | | | | | |
Collapse
|
12
|
Kawakami R, Satomura T, Sakuraba H, Ohshima T. l-Proline dehydrogenases in hyperthermophilic archaea: distribution, function, structure, and application. Appl Microbiol Biotechnol 2011; 93:83-93. [DOI: 10.1007/s00253-011-3682-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/11/2011] [Accepted: 10/27/2011] [Indexed: 10/15/2022]
|
13
|
Shibahara T, Satomura T, Kawakami R, Ohshima T, Sakuraba H. Crystallization and preliminary X-ray analysis of a dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1425-7. [PMID: 22102248 DOI: 10.1107/s1744309111036098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 09/05/2011] [Indexed: 11/11/2022]
Abstract
A dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix was crystallized using the hanging-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 63.4, b = 119.4, c = 70.2 Å, β = 112.0°, and diffracted to 2.0 Å resolution on the BL26B1 beamline at SPring-8. The overall R(merge) was 4.5% and the completeness was 99.8%.
Collapse
Affiliation(s)
- Takenori Shibahara
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Kita-gun, Kagawa 761-0795, Japan
| | | | | | | | | |
Collapse
|