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Moreno Prieto ES, Fjermedal S, Siebenhaar S, Vuillemin M, Holck J, Vincentelli R, Gippert GP, Wilkens C, Morth JP, Henrissat B. Characterization and structural study of a novel β-N-acetylgalactosaminidase from Niabella aurantiaca. FEBS J 2024; 291:1439-1456. [PMID: 38129294 DOI: 10.1111/febs.17042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/06/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
We report here the identification, characterization and three-dimensional (3D) structure determination of NaNga, a newly identified β-N-acetylgalactosaminidase from the Gram-negative soil bacterium Niabella aurantiaca DSM 17617. When recombinantly expressed in Escherichia coli, the enzyme selectively cleaved 4-nitrophenyl-N-acetyl-β-d-galactosamine (pNP-β-d-GalpNAc). The X-ray crystal structure of the protein was refined to 2.5 Å and consists of an N-terminal β-sandwich domain and a (β/α)8 barrel catalytic domain. Despite a mere 22% sequence identity, the 3D structure of NaNga is similar to those previously determined for family GH123 members, suggesting it also employs the same substrate-assisted catalytic mechanism. Inhibition by N-acetyl-galactosamine thiazoline (GalNAc-thiazoline) supports the suggested mechanism. A phylogenetic analysis of its proximal sequence space shows significant clustering of unknown sequences around NaNga with sufficient divergence with previously identified GH123 members to subdivide this family into distinct subfamilies. Although the actual biological substrate of our enzyme remains unknown, examination of the active site pocket suggests that it may be a β-N-acetylgalactosaminide substituted by a monosaccharide at O-3. Analysis of the genomic context suggests, in turn, that this substituted β-N-acetylgalactosaminide may be appended to a d-arabinan from an environmental Actinomycete.
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Affiliation(s)
| | - Sune Fjermedal
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Suzana Siebenhaar
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marlène Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, France
| | - Garry P Gippert
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Vuillemin M, Moreno Prieto ES, Pilgaard B, Siebenhaar S, Holck J, Henrissat B, Bahieldin A, Hakeem KR, Alghamdi KM. Biochemical exploration of family GH119 reveals a single α-amylase specificity and confirms shared catalytic machinery with GH57 enzymes. Int J Biol Macromol 2024; 262:129783. [PMID: 38280706 DOI: 10.1016/j.ijbiomac.2024.129783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 01/29/2024]
Abstract
While hundreds of starch- and glycogen-degrading enzymes have been characterized experimentally in historical families such as GH13, GH14, GH15, GH57 and GH126 of the CAZy database (www.cazy.org), the α-amylase from Bacillus circulans is the only enzyme that has been characterized in family GH119. Since glycosidase families have been shown to often group enzymes with different substrates or products, a single characterized enzyme in a family is insufficient to extrapolate enzyme function based solely on sequence similarity. Here we report the rational exploration of family GH119 through the biochemical characterization of five GH119 members. All enzymes shared single α-amylase specificity but display distinct product profile. We also report the first kinetic constants in family GH119 and the first experimental validation of previously predicted catalytic residues in family GH119, confirming that families GH119 and GH57 can be grouped in the novel clan GH-T of the CAZy database.
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Affiliation(s)
- Marlene Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Eduardo S Moreno Prieto
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Bo Pilgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Suzana Siebenhaar
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark.
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Public Health, Daffodil International University, Dhaka 1341, Bangladesh; Centre of Research Impact and Outcome, Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura 140401, Punjab, India.
| | - Khalid M Alghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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Kristensen SS, Lukassen MV, Siebenhaar S, Diep DB, Morth JP, Mathiesen G. Lactiplantibacillus plantarum as a novel platform for production and purification of integral membrane proteins using RseP as the benchmark. Sci Rep 2023; 13:14361. [PMID: 37658186 PMCID: PMC10474122 DOI: 10.1038/s41598-023-41559-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023] Open
Abstract
The present study describes a detailed procedure for expressing and purifying the integral membrane protein RseP using the pSIP system and Lactiplantibacillus plantarum as an expression host. RseP is a membrane-bound site-2-protease and a known antibacterial target in multiple human pathogens. In the present study, we screened five RseP orthologs from Gram-positive bacteria and found RseP from Enterococcus faecium (EfmRseP) to yield the highest protein levels. The production conditions were optimized and EfmRseP was purified by immobilized metal ion affinity chromatography followed by size-exclusion chromatography. The purification resulted in an overall yield of approximately 1 mg of pure protein per 3 g of wet-weight cell pellet. The structural integrity of the purified protein was confirmed using circular dichroism. We further assessed the expression and purification of RseP from E. faecium in the Gram-negative Escherichia coli. Detection of soluble protein failed in two of the three E. coli strains tested. Purification of EfmRseP expressed in E. coli C43(DE3) resulted in a protein with lower purity compared to EfmRseP expressed in L. plantarum. To our knowledge, this is the first time L. plantarum and the pSIP expression system have been applied for the production of membrane proteins.
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Affiliation(s)
- Sofie S Kristensen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
| | - Marie V Lukassen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Suzana Siebenhaar
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Dzung B Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - J Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), Kongens Lyngby, Denmark.
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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