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Richter AA, Kobus S, Czech L, Hoeppner A, Zarzycki J, Erb TJ, Lauterbach L, Dickschat JS, Bremer E, Smits SHJ. The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine. J Biol Chem 2020; 295:2822-2838. [PMID: 31969391 DOI: 10.1074/jbc.ra119.011277] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/19/2020] [Indexed: 12/17/2022] Open
Abstract
Ectoine is a solute compatible with the physiologies of both prokaryotic and eukaryotic cells and is widely synthesized by bacteria as an osmotic stress protectant. Because it preserves functional attributes of proteins and macromolecular complexes, it is considered a chemical chaperone and has found numerous practical applications. However, the mechanism of its biosynthesis is incompletely understood. The second step in ectoine biosynthesis is catalyzed by l-2,4-diaminobutyrate acetyltransferase (EctA; EC 2.3.1.178), which transfers the acetyl group from acetyl-CoA to EctB-formed l-2,4-diaminobutyrate (DAB), yielding N-γ-acetyl-l-2,4-diaminobutyrate (N-γ-ADABA), the substrate of ectoine synthase (EctC). Here, we report the biochemical and structural characterization of the EctA enzyme from the thermotolerant bacterium Paenibacillus lautus (Pl). We found that (Pl)EctA forms a homodimer whose enzyme activity is highly regiospecific by producing N-γ-ADABA but not the ectoine catabolic intermediate N-α-acetyl-l-2,4-diaminobutyric acid. High-resolution crystal structures of (Pl)EctA (at 1.2-2.2 Å resolution) (i) for its apo-form, (ii) in complex with CoA, (iii) in complex with DAB, (iv) in complex with both CoA and DAB, and (v) in the presence of the product N-γ-ADABA were obtained. To pinpoint residues involved in DAB binding, we probed the structure-function relationship of (Pl)EctA by site-directed mutagenesis. Phylogenomics shows that EctA-type proteins from both Bacteria and Archaea are evolutionarily highly conserved, including catalytically important residues. Collectively, our biochemical and structural findings yielded detailed insights into the catalytic core of the EctA enzyme that laid the foundation for unraveling its reaction mechanism.
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Affiliation(s)
- Alexandra A Richter
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Stefanie Kobus
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany; Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Lukas Lauterbach
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, D-53121 Bonn, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany; SYNMIKRO Research Center, Philipps-University Marburg, D-35043 Marburg, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany; Institute of Biochemistry, Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis. Sci Rep 2019; 9:364. [PMID: 30674920 PMCID: PMC6344544 DOI: 10.1038/s41598-018-36247-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/16/2018] [Indexed: 11/26/2022] Open
Abstract
Ectoine synthase (EctC) is the signature enzyme for the production of ectoine, a compatible solute and chemical chaperone widely synthesized by bacteria as a cellular defense against the detrimental effects of osmotic stress. EctC catalyzes the last step in ectoine synthesis through cyclo-condensation of the EctA-formed substrate N-gamma-acetyl-L-2,4-diaminobutyric acid via a water elimination reaction. We have biochemically and structurally characterized the EctC enzyme from the thermo-tolerant bacterium Paenibacillus lautus (Pl). EctC is a member of the cupin superfamily and forms dimers, both in solution and in crystals. We obtained high-resolution crystal structures of the (Pl)EctC protein in forms that contain (i) the catalytically important iron, (ii) iron and the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid, and (iii) iron and the enzyme reaction product ectoine. These crystal structures lay the framework for a proposal for the EctC-mediated water-elimination reaction mechanism. Residues involved in coordinating the metal, the substrate, or the product within the active site of ectoine synthase are highly conserved among a large group of EctC-type proteins. Collectively, the biochemical, mutational, and structural data reported here yielded detailed insight into the structure-function relationship of the (Pl)EctC enzyme and are relevant for a deeper understanding of the ectoine synthase family as a whole.
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Kobus S, Widderich N, Hoeppner A, Bremer E, Smits SHJ. Overproduction, crystallization and X-ray diffraction data analysis of ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1027-32. [PMID: 26249694 DOI: 10.1107/s2053230x15011115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/08/2015] [Indexed: 11/10/2022]
Abstract
Ectoine biosynthetic genes (ectABC) are widely distributed in bacteria. Microorganisms that carry them make copious amounts of ectoine as a cell protectant in response to high-osmolarity challenges. Ectoine synthase (EctC; EC 4.2.1.108) is the key enzyme for the production of this compatible solute and mediates the last step of ectoine biosynthesis. It catalyzes the ring closure of the cyclic ectoine molecule. A codon-optimized version of ectC from Sphingopyxis alaskensis (Sa) was used for overproduction of SaEctC protein carrying a Strep-tag II peptide at its carboxy-terminus. The recombinant SaEctC-Strep-tag II protein was purified to near-homogeneity from Escherichia coli cell extracts by affinity chromatography. Size-exclusion chromatography revealed that it is a dimer in solution. The SaEctC-Strep-tag II protein was crystallized using the sitting-drop vapour-diffusion method and crystals that diffracted to 1.0 Å resolution were obtained.
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Affiliation(s)
- Stefanie Kobus
- Crystal Farm and X-ray Facility, Heinrich-Heine-University, Universitaetsstrasse 1, 40225 Düsseldorf, Germany
| | - Nils Widderich
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, 35043 Marburg, Germany
| | - Astrid Hoeppner
- Crystal Farm and X-ray Facility, Heinrich-Heine-University, Universitaetsstrasse 1, 40225 Düsseldorf, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, 35043 Marburg, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University, Universitaetsstrasse 1, 40225 Düsseldorf, Germany
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Höppner A, Widderich N, Lenders M, Bremer E, Smits SHJ. Crystal structure of the ectoine hydroxylase, a snapshot of the active site. J Biol Chem 2014; 289:29570-83. [PMID: 25172507 DOI: 10.1074/jbc.m114.576769] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Ectoine and its derivative 5-hydroxyectoine are compatible solutes that are widely synthesized by bacteria to cope physiologically with osmotic stress. They also serve as chemical chaperones and maintain the functionality of macromolecules. 5-Hydroxyectoine is produced from ectoine through a stereo-specific hydroxylation, an enzymatic reaction catalyzed by the ectoine hydroxylase (EctD). The EctD protein is a member of the non-heme-containing iron(II) and 2-oxoglutarate-dependent dioxygenase superfamily and is evolutionarily well conserved. We studied the ectoine hydroxylase from the cold-adapted marine ultra-microbacterium Sphingopyxis alaskensis (Sa) and found that the purified SaEctD protein is a homodimer in solution. We determined the SaEctD crystal structure in its apo-form, complexed with the iron catalyst, and in a form that contained iron, the co-substrate 2-oxoglutarate, and the reaction product of EctD, 5-hydroxyectoine. The iron and 2-oxoglutarate ligands are bound within the EctD active site in a fashion similar to that found in other members of the dioxygenase superfamily. 5-Hydroxyectoine, however, is coordinated by EctD in manner different from that found in high affinity solute receptor proteins operating in conjunction with microbial import systems for ectoines. Our crystallographic analysis provides a detailed view into the active site of the ectoine hydroxylase and exposes an intricate network of interactions between the enzyme and its ligands that collectively ensure the hydroxylation of the ectoine substrate in a position- and stereo-specific manner.
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Affiliation(s)
- Astrid Höppner
- From the X-ray Facility and Crystal Farm, Heinrich-Heine-University at Düsseldorf, D-40225 Düsseldorf
| | - Nils Widderich
- the Department of Biology, Laboratory for Microbiology, Philipps-University at Marburg, D-35043 Marburg, the Max Planck Institute for Terrestrial Microbiology, Emeritus Group R. K. Thauer, D-35043 Marburg
| | - Michael Lenders
- the Institute of Biochemistry, Heinrich-Heine-University at Düsseldorf, D-40225 Düsseldorf, and
| | - Erhard Bremer
- the Department of Biology, Laboratory for Microbiology, Philipps-University at Marburg, D-35043 Marburg, the LOEWE-Center for Synthetic Microbiology, Philipps-University at Marburg, D-35043 Marburg, Germany
| | - Sander H J Smits
- the Institute of Biochemistry, Heinrich-Heine-University at Düsseldorf, D-40225 Düsseldorf, and
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