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Boucher L, Somani S, Negron C, Ma W, Jacobs S, Chan W, Malia T, Obmolova G, Teplyakov A, Gilliland GL, Luo J. Surface salt bridges contribute to the extreme thermal stability of an FN3-like domain from a thermophilic bacterium. Proteins 2021; 90:270-281. [PMID: 34405904 DOI: 10.1002/prot.26218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 03/08/2021] [Accepted: 08/02/2021] [Indexed: 12/27/2022]
Abstract
This study uses differential scanning calorimetry, X-ray crystallography, and molecular dynamics simulations to investigate the structural basis for the high thermal stability (melting temperature 97.5°C) of a FN3-like protein domain from thermophilic bacteria Thermoanaerobacter tengcongensis (FN3tt). FN3tt adopts a typical FN3 fold with a three-stranded beta sheet packing against a four-stranded beta sheet. We identified three solvent exposed arginine residues (R23, R25, and R72), which stabilize the protein through salt bridge interactions with glutamic acid residues on adjacent strands. Alanine mutation of the three arginine residues reduced melting temperature by up to 22°C. Crystal structures of the wild type (WT) and a thermally destabilized (∆Tm -19.7°C) triple mutant (R23L/R25T/R72I) were found to be nearly identical, suggesting that the destabilization is due to interactions of the arginine residues. Molecular dynamics simulations showed that the salt bridge interactions in the WT were stable and provided a dynamical explanation for the cooperativity observed between R23 and R25 based on calorimetry measurements. In addition, folding free energy changes computed using free energy perturbation molecular dynamics simulations showed high correlation with melting temperature changes. This work is another example of surface salt bridges contributing to the enhanced thermal stability of thermophilic proteins. The molecular dynamics simulation methods employed in this study may be broadly useful for in silico surface charge engineering of proteins.
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Affiliation(s)
- Lauren Boucher
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Sandeep Somani
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | | | - Wenting Ma
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Steven Jacobs
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Winnie Chan
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Thomas Malia
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Galina Obmolova
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Alexey Teplyakov
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Gary L Gilliland
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Jinquan Luo
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
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2
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Liu W, Ma C, Liu W, Zheng Y, Chen CC, Liang A, Luo X, Li Z, Ma W, Song Y, Guo RT, Zhang T. Functional and structural investigation of a novel β-mannanase BaMan113A from Bacillus sp. N16-5. Int J Biol Macromol 2021; 182:899-909. [PMID: 33865894 DOI: 10.1016/j.ijbiomac.2021.04.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Abstract
Mannan is an important renewable resource whose backbone can be hydrolyzed by β-mannanases to generate manno-oligosaccharides of various sizes. Only a few glycoside hydrolase (GH) 113 family β-mannanases have been functionally and structurally characterize. Here, we report the function and structure of a novel GH113 β-mannanase from Bacillus sp. N16-5 (BaMan113A). BaMan113A exhibits a substrate preference toward manno-oligosaccharides and releases mannose and mannobiose as main hydrolytic products. The crystal structure of BaMan113A suggest that the enzyme shows a semi-enclosed substrate-binding cleft and the amino acids surrounding the +2 subsite form a steric barrier to terminate the substrate-binding tunnel. Based on these structural features, we conducted mutagenesis to engineer BaMan113A to remove the steric hindrance of the substrate-binding tunnel. We found that F101E and N236Y variants exhibit increased specific activity toward mannans comparing to the wild-type enzyme. Meanwhile, the product profiles of these two variants toward polysaccharides changed from mannose to a series of manno-oligosaccharides. The crystal structure of variant N236Y was also determined to illustrate the molecular basis underlying the mutation. In conclusion, we report the functional and structural features of a novel GH113 β-mannanase, and successfully improved its endo-acting activity by using structure-based engineering.
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Affiliation(s)
- Wenting Liu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Cuiping Ma
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Weidong Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yingying Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ailing Liang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xuegang Luo
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhongyuan Li
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenjian Ma
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yajian Song
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Tongcun Zhang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
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Sakaguchi M, Mukaeda H, Kume A, Toyoda Y, Sakoh T, Kawakita M. Evaluation of the roles of hydrophobic residues in the N-terminal region of archaeal trehalase in its folding. Appl Microbiol Biotechnol 2021; 105:3181-3194. [PMID: 33791835 DOI: 10.1007/s00253-021-11237-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/01/2021] [Accepted: 03/14/2021] [Indexed: 11/30/2022]
Abstract
Thermoplasma trehalase Tvn1315 is predicted to be composed of a β-sandwich domain (BD) and a catalytic domain (CD) based on the structure of the bacterial GH15 family glucoamylase (GA). Tvn1315 as well as Tvn1315 (Δ5), in which the 5 N-terminal amino acids are deleted, could be expressed in Escherichia coli as active enzymes, but deletion of 10 residues (Δ10) led to inclusion body formation. To further investigate the role of the N-terminal region of BD, we constructed five mutants of Δ5, in which each of the 5th to 10th residues of the N-terminus of Tvn1315 was mutated to Ala. Every mutant protein could be recovered in soluble form, but only a small fraction of the Y9A mutant was recovered in the soluble fraction. The Y9A mutant recovered in soluble form had similar specific activity to the other proteins. Subsequent mutation analysis at the 9th position of Tvn1315 in Δ5 revealed that aromatic as well as bulky hydrophobic residues could function properly, but residues with hydroxy groups impaired the solubility. Similar results were obtained with mutants based on untruncated Tvn1315. When the predicted BD, Δ5BD, Δ10BD, and BD mutants were expressed, the Δ10BD protein formed inclusion bodies, and the BD mutants behaved similarly to the Δ5 and full-length enzyme mutants. These results suggest that the hydrophobic region is involved in the solubilization of BD during the folding process. Taken together, these results indicate that the solubility of CD depends on BD folding. KEY POINTS: • N-terminal hydrophobic region of the BD is involved in the protein folding. • The N-terminal hydrophobic region of the BD is also involved in the BD folding. • BD is able to weakly interact with the insoluble β-glucan.
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Affiliation(s)
- Masayoshi Sakaguchi
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan.
| | - Hinako Mukaeda
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Anna Kume
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Yukiko Toyoda
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Takumi Sakoh
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Masao Kawakita
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
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Honda S, Kimura M, Wakita S, Oka Y, Kawakita M, Oyama F, Sakaguchi M. The Listeria innocua chitinase LinChi78 has a unique region that is necessary for hydrolytic activity. Appl Microbiol Biotechnol 2019; 103:1777-1787. [PMID: 30610281 DOI: 10.1007/s00253-018-9573-5] [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: 08/24/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 10/27/2022]
Abstract
Chitinases are generally composed of multiple domains; a catalytic domain and one or more additional domains that are not absolutely required but may modify the chitinolytic activity. The LinChi78 chitinase from Listeria innocua has a catalytic domain (CatD), a fibronectin type III-like (FnIII) domain, a chitin-binding domain (ChBD), and an unknown-function region (UFR) located between the CatD and FnIII domains. The UFR is 146 amino acid residues in length and does not have a homologous domain in the Conserved Domain Database. We performed a functional analysis of these domains and the UFR using several C-terminally and internally deleted mutants of LinChi78. Hydrolysis of an artificial substrate was almost unaffected by deletion of the ChBD and/or the FnIII domain, although the ChBD-deleted enzymes were approximately 30% less active toward colloidal chitin than LinChi78. On the other hand, deletion of the UFR led to an extensive loss of chitinase activity toward an artificial substrate as well as polymeric substrates. Upon further analysis, we found that the GKQTI stretch, between the 567th (G) and 571th (I) amino acid residues, in the UFR is critical for LinChi78 activity and demonstrated that Gln569 and Ile571 play central roles in eliciting this activity. Taken together, these results indicated that LinChi78 has a unique catalytic region composed of a typical CatD and an additional region that is essential for activity. Characterization of the unique catalytic region of LinChi78 will improve our understanding of GH18 chitinases.
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Affiliation(s)
- Shotaro Honda
- Department of Chemistry and Life Science, Kogakuin University, 2665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Masahiro Kimura
- Department of Chemistry and Life Science, Kogakuin University, 2665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Satoshi Wakita
- Department of Chemistry and Life Science, Kogakuin University, 2665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Yuji Oka
- Department of Chemistry and Life Science, Kogakuin University, 2665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Masao Kawakita
- Department of Chemistry and Life Science, Kogakuin University, 2665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Fumitaka Oyama
- Department of Chemistry and Life Science, Kogakuin University, 2665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Masayoshi Sakaguchi
- Department of Chemistry and Life Science, Kogakuin University, 2665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan.
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5
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Sakaguchi M, Matsushima Y, Nagamine Y, Matsuhashi T, Honda S, Okuda S, Ohno M, Sugahara Y, Shin Y, Oyama F, Kawakita M. Functional dissection of the N-terminal sequence of Clostridium sp. G0005 glucoamylase: identification of components critical for folding the catalytic domain and for constructing the active site structure. Appl Microbiol Biotechnol 2016; 101:2415-2425. [PMID: 27942757 DOI: 10.1007/s00253-016-8024-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/06/2016] [Accepted: 11/22/2016] [Indexed: 11/30/2022]
Abstract
Clostridium sp. G0005 glucoamylase (CGA) is composed of a β-sandwich domain (BD), a linker, and a catalytic domain (CD). In the present study, CGA was expressed in Escherichia coli as inclusion bodies when the N-terminal region (39 amino acid residues) of the BD was truncated. To further elucidate the role of the N-terminal region of the BD, we constructed N-terminally truncated proteins (Δ19, Δ24, Δ29, and Δ34) and assessed their solubility and activity. Although all evaluated proteins were soluble, their hydrolytic activities toward maltotriose as a substrate varied: Δ19 and Δ24 were almost as active as CGA, but the activity of Δ29 was substantially lower, and Δ34 exhibited little hydrolytic activity. Subsequent truncation analysis of the N-terminal region sequence between residues 25 and 28 revealed that truncation of less than 26 residues did not affect CGA activity, whereas truncation of 26 or more residues resulted in a substantial loss of activity. Based on further site-directed mutagenesis and N-terminal sequence analysis, we concluded that the 26XaaXaaTrp28 sequence of CGA is important in exhibiting CGA activity. These results suggest that the N-terminal region of the BD in bacterial GAs may function not only in folding the protein into the correct structure but also in constructing a competent active site for catalyzing the hydrolytic reaction.
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Affiliation(s)
- Masayoshi Sakaguchi
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan.
| | - Yudai Matsushima
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Yusuke Nagamine
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Tomoki Matsuhashi
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Shotaro Honda
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Shoi Okuda
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Misa Ohno
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Yasusato Sugahara
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Yongchol Shin
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Fumitaka Oyama
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Masao Kawakita
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kami-kitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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Wang G, Wu J, Lin J, Ye X, Yao B. The disruption of two salt bridges of the cold-active xylanase XynGR40 results in an increase in activity, but a decrease in thermostability. Biochem Biophys Res Commun 2016; 481:139-145. [DOI: 10.1016/j.bbrc.2016.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022]
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A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1436-43. [PMID: 27456266 DOI: 10.1016/j.bbapap.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/11/2016] [Accepted: 07/15/2016] [Indexed: 11/20/2022]
Abstract
Structural comparisons of the cold adapted subtilase VPR and its thermophilic homologue, aqualysin I (AQUI) indicated the presence of additional salt bridges in the latter. Few of those appear to contribute significantly to thermal stability of AQUI. This includes a putative salt bridge between residues Lys142 and Glu172 as its deletion did not have any significant effect on its stability or activity (Jónsdóttir et al. (2014)). Insertion of this putative salt bridge into the structure of VPR, in a double mutant (VPRΔC_Q142K/S172E), however was detrimental to the stability of the enzyme. Incorporation of either the Q142K or S172E mutations into VPR, were found to significantly affect the catalytic properties of the enzyme. The single mutation Q142K was highly effective, as it increased the kcat and kcat/Km more than twofold. When the Q142K mutation was inserted into a thermostabilized, but a low activity mutant of VPR (VPRΔC_N3P/I5P), the activity increased about tenfold in terms of kcat and kcat/Km, while retaining the stability of the mutant. Molecular dynamics simulations of the single mutants were carried out to provide structural rationale for these experimental observations. Based on root mean square fluctuation (RMSF) profiles, the two mutants were more flexible in certain regions of the structure and the Q142K mutant had the highest overall flexibility of the three enzymes. The results suggest that weakening of specific H-bonds resulting from the mutations may be propagated over some distance giving rise to higher flexibility in the active site regions of the enzyme, causing higher catalytic activity in the mutants.
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Vojcic L, Pitzler C, Körfer G, Jakob F, Ronny Martinez, Maurer KH, Schwaneberg U. Advances in protease engineering for laundry detergents. N Biotechnol 2015; 32:629-34. [PMID: 25579194 DOI: 10.1016/j.nbt.2014.12.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/02/2014] [Accepted: 12/31/2014] [Indexed: 02/03/2023]
Abstract
Proteases are essential ingredients in modern laundry detergents. Over the past 30 years, subtilisin proteases employed in the laundry detergent industry have been engineered by directed evolution and rational design to tailor their properties towards industrial demands. This comprehensive review discusses recent success stories in subtilisin protease engineering. Advances in protease engineering for laundry detergents comprise simultaneous improvement of thermal resistance and activity at low temperatures, a rational strategy to modulate pH profiles, and a general hypothesis for how to increase promiscuous activity towards the production of peroxycarboxylic acids as mild bleaching agents. The three protease engineering campaigns presented provide in-depth analysis of protease properties and have identified principles that can be applied to improve or generate enzyme variants for industrial applications beyond laundry detergents.
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Affiliation(s)
- Ljubica Vojcic
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | | | | | - Felix Jakob
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, D-52074 Aachen, Germany
| | - Ronny Martinez
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany; EW-Nutrition GmbH, Enzyme Technology, Nattermannallee 1, D-50829 Köln, Germany
| | | | - Ulrich Schwaneberg
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany; DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, D-52074 Aachen, Germany.
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