1
|
Koeppl LH, Popadić D, Saleem-Batcha R, Germer P, Andexer JN. Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases. Commun Biol 2024; 7:380. [PMID: 38548921 PMCID: PMC10978960 DOI: 10.1038/s42003-024-06078-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 03/20/2024] [Indexed: 04/01/2024] Open
Abstract
S-Adenosyl-L-homocysteine hydrolase (SAHH) reversibly cleaves S-adenosyl-L-homocysteine, the product of S-adenosyl-L-methionine-dependent methylation reactions. The conversion of S-adenosyl-L-homocysteine into adenosine and L-homocysteine plays an important role in the regulation of the methyl cycle. An alternative metabolic route for S-adenosyl-L-methionine regeneration in the extremophiles Methanocaldococcus jannaschii and Thermotoga maritima has been identified, featuring the deamination of S-adenosyl-L-homocysteine to S-inosyl-L-homocysteine. Herein, we report the structural characterisation of different archaeal SAHHs together with a biochemical analysis of various SAHHs from all three domains of life. Homologues deriving from the Euryarchaeota phylum show a higher conversion rate with S-inosyl-L-homocysteine compared to S-adenosyl-L-homocysteine. Crystal structures of SAHH originating from Pyrococcus furiosus in complex with SLH and inosine as ligands, show architectural flexibility in the active site and offer deeper insights into the binding mode of hypoxanthine-containing substrates. Altogether, the findings of our study support the understanding of an alternative metabolic route for S-adenosyl-L-methionine and offer insights into the evolutionary progression and diversification of SAHHs involved in methyl and purine salvage pathways.
Collapse
Affiliation(s)
- Lars-Hendrik Koeppl
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Désirée Popadić
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Raspudin Saleem-Batcha
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Philipp Germer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany.
| |
Collapse
|
2
|
Brzezinski K, Czyrko J, Sliwiak J, Nalewajko-Sieliwoniuk E, Jaskolski M, Nocek B, Dauter Z. S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive form - Biochemical and structural studies. Int J Biol Macromol 2017; 104:584-596. [PMID: 28629859 PMCID: PMC7888557 DOI: 10.1016/j.ijbiomac.2017.06.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 11/26/2022]
Abstract
Thermotoga maritima is a hyperthermophilic bacterium but its genome encodes a number of archaeal proteins including S-adenosyl-L-homocysteine hydrolase (SAHase), which regulates cellular methylation reactions. The question of proper folding and activity of proteins of extremophilic origin is an intriguing problem. When expressed in E.coli and purified (as a homotetramer) at room temperature, the hyperthermophilic SAHase from T.maritima was inactive. ITC study indicated that the protein undergoes heat-induced conformational changes, and enzymatic activity assays demonstrated that these changes are required to attain enzymatic activity. To explain the mechanism of thermal activation, two crystal structures of the inactive form of T. maritima SAHase (iTmSAHase) were determined for an incomplete binary complex with the reduced cofactor (NADH), and in a mixture of binary complexes with NADH and with adenosine. In contrast to active SAHases, in iTmSAHase only two of the four subunits contain a bound cofactor, predominantly in its non-reactive, reduced state. Moreover, the closed-like conformation of the cofactor-containing subunits precludes substrate delivery to the active site. The two other subunits cannot be involved in the enzymatic reaction either; although they have an open-like conformation, they do not contain the cofactor, whose binding site may be occupied by an adenosine molecule. The results suggest that this enzyme, when expressed in mesophilic cells, is arrested in the activity-incompatible conformation revealed by its crystal structures.
Collapse
Affiliation(s)
- Krzysztof Brzezinski
- Institute of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland.
| | - Justyna Czyrko
- Institute of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | | | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
| | - Boguslaw Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| |
Collapse
|
3
|
Zheng Y, Chen CC, Ko TP, Xiao X, Yang Y, Huang CH, Qian G, Shao W, Guo RT. Crystal structures of S-adenosylhomocysteine hydrolase from the thermophilic bacterium Thermotoga maritima. J Struct Biol 2015; 190:135-42. [PMID: 25791616 DOI: 10.1016/j.jsb.2015.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/18/2015] [Accepted: 03/04/2015] [Indexed: 11/17/2022]
Abstract
S-adenosylhomocysteine (SAH) hydrolase catalyzes the reversible hydrolysis of SAH into adenosine and homocysteine by using NAD(+) as a cofactor. The enzyme from Thermotoga maritima (tmSAHH) has great potentials in industrial applications because of its hyperthermophilic properties. Here, two crystal structures of tmSAHH in complex with NAD(+) show both open and closed conformations despite the absence of bound substrate. Each subunit of the tetrameric enzyme is composed of three domains, namely the catalytic domain, the NAD(+)-binding domain and the C-terminal domain. The NAD(+) binding mode is clearly observed and a substrate analogue can also be modeled into the active site, where two cysteine residues in mesophilic enzymes are replaced by serine and threonine in tmSAHH. Notably, the C-terminal domain of tmSAHH lacks the second loop region of mesophilic SAHH, which is important in NAD(+) binding, and thus exposes the bound cofactor to the solvent. The difference explains the higher NAD(+) requirement of tmSAHH because of the reduced affinity. Furthermore, the feature of missing loop is consistently observed in thermophilic bacterial and archaeal SAHHs, and may be related to their thermostability.
Collapse
Affiliation(s)
- Yingying Zheng
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chun-Chi Chen
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Xiansha Xiao
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yunyun Yang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chun-Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Guojun Qian
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang 212013, China
| | - Weilan Shao
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang 212013, China.
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| |
Collapse
|
4
|
He M, Zheng Y, Huang CH, Qian G, Xiao X, Ko TP, Shao W, Guo RT. Crystallization and preliminary X-ray diffraction analysis of the S-adenosylhomocysteine hydrolase (SAHH) from Thermotoga maritima. Acta Crystallogr F Struct Biol Commun 2014; 70:1563-5. [PMID: 25372832 PMCID: PMC4231867 DOI: 10.1107/s2053230x14013478] [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] [Received: 03/28/2014] [Accepted: 06/10/2014] [Indexed: 11/10/2022] Open
Abstract
S-Adenosylhomocysteine hydrolase (SAHH) catalyzes the reversible conversion of S-adenosylhomocysteine into adenosine and homocysteine. The SAHH from Thermotoga maritima (TmSAHH) was expressed in Escherichia coli and the recombinant protein was purified and crystallized. TmSAHH crystals belonging to space group C2, with unit-cell parameters a=106.3, b=112.0, c=164.9 Å, β=103.5°, were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.85 Å resolution. Initial phase determination by molecular replacement clearly indicated that the crystal contains one homotetramer per asymmetric unit. Further refinement of the crystal structure is in progress.
Collapse
Affiliation(s)
- Miao He
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People’s Republic of China
| | - Yingying Zheng
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Chun-Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Guojun Qian
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang 212013, People’s Republic of China
| | - Xiansha Xiao
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Weilan Shao
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang 212013, People’s Republic of China
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| |
Collapse
|
5
|
Xue F, Liu ZQ, Wan NW, Zheng YG. Purification, gene cloning, and characterization of a novel halohydrin dehalogenase from Agromyces mediolanus ZJB120203. Appl Biochem Biotechnol 2014; 174:352-64. [PMID: 25069405 DOI: 10.1007/s12010-014-1111-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/22/2014] [Indexed: 11/29/2022]
Abstract
A novel halohydrin dehalogenase (HHDH), catalyzing the transformation of 1,3-dichloro-2-propanol (1,3-DCP) to epichlorohydrin (ECH), was purified from Agromyces mediolanus ZJB120203. The molecular mass of the enzyme was estimated to be 28 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). A 735-bp nucleotide fragment was obtained based on the N-terminal and internal amino acid sequences of the purified HHDH. The gene codes a protein sequence with 244 amino acid residues, and the protein sequence shows high similarity to Hhe AAD2 (HHDH from Arthrobacter sp. AD2), defined as Hhe AAm, which is the seventh reported HHDH. Expression of Hhe AAm was carried out in Escherichia coli and purification was performed by nickel-affinity chromatography. The recombinant HheAAm possessed an optimal pH of 8.5 and an optimal temperature of 50 °C and manifested a K m of 4.58 mM and a V max of 3.84 μmol/min(/)mg. The activity of Hhe AAm was not significantly affected by metal ions such as Zn(2+), Ca(2+), Cu(2+), and EDTA, but was strongly inhibited by Hg(2+) and Ag(+). In particular, the Hhe AAm exhibits an enantioselectivity for the conversion of prochiral 1,3-DCP to (S)-ECH. The applications of the Hhe AAm as a catalyst for asymmetric synthesis are promising.
Collapse
Affiliation(s)
- Feng Xue
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | | | | | | |
Collapse
|
6
|
A thermostable S-adenosylhomocysteine hydrolase from Thermotoga maritima: properties and its application on S-adenosylhomocysteine production with enzymatic cofactor regeneration. Enzyme Microb Technol 2014; 64-65:33-7. [PMID: 25152414 DOI: 10.1016/j.enzmictec.2014.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/27/2014] [Accepted: 06/30/2014] [Indexed: 11/20/2022]
Abstract
S-adenosylhomocysteine (SAH) is an effective sedative, a good sleep modulator, and a new anticonvulsant. SAH can be synthesized from adenosine and homocysteine by using microbial S-adenosylhomocysteine hydrolase (SAHase). The extremely thermostable SAHase and lactate dehydrogenase (LDH) from Thermotoga maritima were successfully overexpressed in Escherichia coli, and purified by heat treatments. The SAHase exhibited the highest activity at 85 °C and pH 8.0 with a specific activity of 6.2 U/mg when NAD concentration was 1mM. However, optimal SAHase reaction conditions shifted to 100 °C and pH 11.2, and its specific activity increased to 36.8 U/mg after NAD concentration was raised to 8mM. Biosynthesis of SAH at 85 °C largely increased the adenosine solubility which was a limiting factor for improving the titer of product. At 85 °C and pH 8.0, 24 μmol of SAH was obtained when 0.5mg of SAHase was applied to a 10 ml reaction mixture. The SAH production was further increased to 153 μmol by adding LDH and pyruvate into the reaction mixture for NAD regeneration. Therefore, extremely thermostable enzymes SAHase and LDH from T. maritima form an efficient NAD consumption and regeneration system for SAH biosynthesis. This method has great potential for industrial-scale enzymatic production of SAH.
Collapse
|