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Lee S, Kim S, Kim IK, Kim KJ. Structural and Biochemical Studies on Product Inhibition of S-Adenosylmethionine Synthetase from Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15692-15700. [PMID: 37846083 DOI: 10.1021/acs.jafc.3c05180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
S-Adenosylmethionine (SAM) acts as a methyl donor in living organisms, and S-adenosylmethionine synthetase (MetK) is an essential enzyme for cells, as it synthesizes SAM from methionine and adenosine triphosphate (ATP). This study determined the crystal structures of the apo form and adenosine/triphosphate complex form of MetK from Corynebacterium glutamicum (CgMetK). Results showed that CgMetK has an allosteric inhibitor binding site for the SAM product in the vicinity of the active site and is inhibited by SAM both competitively and noncompetitively. Through structure-guided protein engineering, the CgMetKE68A variant was developed that exhibited an almost complete release of inhibition by SAM with rather enhanced enzyme activity. The crystal structure of the CgMetKE68A variant revealed that the formation of a new hydrogen bond between Tyr66 and Glu102 by the E68A mutation disrupted the allosteric SAM binding site and also improved the protein thermal stability by strengthening the tetramerization of the enzyme.
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Affiliation(s)
- Seunghwan Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seongmin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Il-Kwon Kim
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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Ma X, Wang L, Yang F, Li J, Guo L, Guo Y, He S. Drug sensitivity and genome-wide analysis of two strains of Mycoplasma gallisepticum with different biofilm intensity. Front Microbiol 2023; 14:1196747. [PMID: 37621399 PMCID: PMC10445764 DOI: 10.3389/fmicb.2023.1196747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Mycoplasma gallisepticum (MG) is one of the major causative agents of chronic respiratory diseases in poultry. The biofilms of MG are highly correlated to its chronic infection. However data on genes involved in biofilm formation ability are still scarse. MG strains with distinct biofilm intensity were screened by crystal violet staining morphotyped and characterized for the drug sensitivity. Two MG strains NX-01 and NX-02 showed contrasted ability to biofilm formation. The biofilm formation ability of NX-01 strain was significantly higher than that of NX-02 strain (p < 0.01). The drug sensitivity test showed that the stronger the ability of MG stain to form biofilms, the weaker its sensitivity to 17 antibiotic drugs. Moreover, putative key genes related to biofilm formation were screened by genome-wide analysis. A total of 13 genes and proteins related to biofilm formation, including ManB, oppA, oppD, PDH, eno, RelA, msbA, deoA, gapA, rpoS, Adhesin P1 precursor, S-adenosine methionine synthetase, and methionyl tRNA synthetase were identified. There were five major discrepancies between the two isolated MG strains and the five NCBI-published MG strains. These findings provide potential targets for inhibiting the formation of biofilm of MG, and lay a foundation for treating chronic infection.
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Affiliation(s)
- Xiaoyan Ma
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Li Wang
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Fei Yang
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Jidong Li
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Lei Guo
- Ningxia Xiaoming Agriculture and Animal Husbandry Co., Ltd., Yinchuan, China
| | - Yanan Guo
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Shenghu He
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
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Kleiner D, Shapiro Tuchman Z, Shmulevich F, Shahar A, Zarivach R, Kosloff M, Bershtein S. Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains. Protein Sci 2022; 31:e4352. [PMID: 35762725 PMCID: PMC9202080 DOI: 10.1002/pro.4352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/14/2022] [Accepted: 05/07/2022] [Indexed: 11/16/2022]
Abstract
Homomers are prevalent in bacterial proteomes, particularly among core metabolic enzymes. Homomerization is often key to function and regulation, and interfaces that facilitate the formation of homomeric enzymes are subject to intense evolutionary change. However, our understanding of the molecular mechanisms that drive evolutionary variation in homomeric complexes is still lacking. How is the diversification of protein interfaces linked to variation in functional regulation and structural integrity of homomeric complexes? To address this question, we studied quaternary structure evolution of bacterial methionine S‐adenosyltransferases (MATs)—dihedral homotetramers formed along a large and conserved dimeric interface harboring two active sites, and a small, recently evolved, interdimeric interface. Here, we show that diversity in the physicochemical properties of small interfaces is directly linked to variability in the kinetic stability of MAT quaternary complexes and in modes of their functional regulation. Specifically, hydrophobic interactions within the small interface of Escherichia coli MAT render the functional homotetramer kinetically stable yet impose severe aggregation constraints on complex assembly. These constraints are alleviated by electrostatic interactions that accelerate dimer‐dimer assembly. In contrast, Neisseria gonorrhoeae MAT adopts a nonfunctional dimeric state due to the low hydrophobicity of its small interface and the high flexibility of its active site loops, which perturbs small interface integrity. Remarkably, in the presence of methionine and ATP, N. gonorrhoeae MAT undergoes substrate‐induced assembly into a functional tetrameric state. We suggest that evolution acts on the interdimeric interfaces of MATs to tailor the regulation of their activity and stability to unique organismal needs. PDB Code(s): 7R2W;7R3B;
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Affiliation(s)
- Daniel Kleiner
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ziva Shapiro Tuchman
- The Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Fannia Shmulevich
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anat Shahar
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Macromolecular Crystallography and Cryo-EM Research Center, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mickey Kosloff
- The Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Glucose oxidase converted into a general sugar-oxidase. Sci Rep 2022; 12:10716. [PMID: 35739181 PMCID: PMC9226012 DOI: 10.1038/s41598-022-14957-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
Entrapment of glucose oxidase (GOx) within metallic gold converts this widely used enzyme into a general saccharide oxidase. The following sugar molecules were oxidized by the entrapped enzyme (in addition to D-glucose): fructose, xylose, L-glucose, glucose-6-phosphate, sucrose, lactose, methylglucoside, and the tri-saccharide raffinose. With the exception of raffinose, none of these sugars have a natural specific oxidase. The origin of this generalization of activity is attributed to the strong protein-gold 3D interactions and to the strong interactions of the co-entrapped CTAB with both the gold, and the protein. It is proposed that these interactions induce conformational changes in the channel leading to the active site, which is located at the interface between the two units of the dimeric GOx protein. The observations are compatible with affecting the specific conformation change of pulling apart and opening this gate-keeper, rendering the active site accessible to a variety of substrates. The entrapment methodology was also found to increase the thermal stability of GOx up to 100 °C and to allow its convenient reuse, two features of practical importance.
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Chouhan BPS, Gade M, Martinez D, Toledo‐Patino S, Laurino P. Implications of divergence of methionine adenosyltransferase in archaea. FEBS Open Bio 2022; 12:130-145. [PMID: 34655277 PMCID: PMC8727953 DOI: 10.1002/2211-5463.13312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 11/12/2022] Open
Abstract
Methionine adenosyltransferase (MAT) catalyzes the biosynthesis of S-adenosyl methionine from l-methionine and ATP. MAT enzymes are ancient, believed to share a common ancestor, and are highly conserved in all three domains of life. However, the sequences of archaeal MATs show considerable divergence compared with their bacterial and eukaryotic counterparts. Furthermore, the structural significance and functional significance of this sequence divergence are not well understood. In the present study, we employed structural analysis and ancestral sequence reconstruction to investigate archaeal MAT divergence. We observed that the dimer interface containing the active site (which is usually well conserved) diverged considerably between the bacterial/eukaryotic MATs and archaeal MAT. A detailed investigation of the available structures supports the sequence analysis outcome: The protein domains and subdomains of bacterial and eukaryotic MAT are more similar than those of archaea. Finally, we resurrected archaeal MAT ancestors. Interestingly, archaeal MAT ancestors show substrate specificity, which is lost during evolution. This observation supports the hypothesis of a common MAT ancestor for the three domains of life. In conclusion, we have demonstrated that archaeal MAT is an ideal system for studying an enzyme family that evolved differently in one domain compared with others while maintaining the same catalytic activity.
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Affiliation(s)
- Bhanu Pratap Singh Chouhan
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Madhuri Gade
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Desirae Martinez
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Saacnicteh Toledo‐Patino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
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Shrestha S, Clark AC. Evolution of the folding landscape of effector caspases. J Biol Chem 2021; 297:101249. [PMID: 34592312 PMCID: PMC8628267 DOI: 10.1016/j.jbc.2021.101249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/07/2022] Open
Abstract
Caspases are a family of cysteinyl proteases that control programmed cell death and maintain homeostasis in multicellular organisms. The caspase family is an excellent model to study protein evolution because all caspases are produced as zymogens (procaspases [PCPs]) that must be activated to gain full activity; the protein structures are conserved through hundreds of millions of years of evolution; and some allosteric features arose with the early ancestor, whereas others are more recent evolutionary events. The apoptotic caspases evolved from a common ancestor (CA) into two distinct subfamilies: monomers (initiator caspases) or dimers (effector caspases). Differences in activation mechanisms of the two subfamilies, and their oligomeric forms, play a central role in the regulation of apoptosis. Here, we examine changes in the folding landscape by characterizing human effector caspases and their CA. The results show that the effector caspases unfold by a minimum three-state equilibrium model at pH 7.5, where the native dimer is in equilibrium with a partially folded monomeric (PCP-7, CA) or dimeric (PCP-6) intermediate. In comparison, the unfolding pathway of PCP-3 contains both oligomeric forms of the intermediate. Overall, the data show that the folding landscape was first established with the CA and was retained for >650 million years. Partially folded monomeric or dimeric intermediates in the ancestral ensemble provide mechanisms for evolutionary changes that affect stability of extant caspases. The conserved folding landscape allows for the fine-tuning of enzyme stability in a species-dependent manner while retaining the overall caspase–hemoglobinase fold.
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Affiliation(s)
- Suman Shrestha
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - A Clay Clark
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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Sekula B, Ruszkowski M, Dauter Z. S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. Int J Biol Macromol 2020; 151:554-565. [PMID: 32057875 DOI: 10.1016/j.ijbiomac.2020.02.100] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
Abstract
S-adenosylmethionine synthases (MATs) are responsible for production of S-adenosylmethionine, the cofactor essential for various methylation reactions, production of polyamines and phytohormone ethylene, etc. Plants have two distinct MAT types (I and II). This work presents the structural analysis of MATs from Arabidopsis thaliana (AtMAT1 and AtMAT2, both type I) and Medicago truncatula (MtMAT3a, type II), which, unlike most MATs from other domains of life, are dimers where three-domain subunits are sandwiched flat with one another. Although MAT types are very similar, their subunits are differently oriented within the dimer. Structural snapshots along the enzymatic reaction reveal the exact conformation of precatalytic methionine in the active site and show a binding niche, characteristic only for plant MATs, that may serve as a lock of the gate loop. Nevertheless, plants, in contrary to mammals, lack the MAT regulatory subunit, and the regulation of plant MAT activity is still puzzling. Our structures open a possibility of an allosteric activity regulation of type I plant MATs by linear compounds, like polyamines, which would tighten the relationship between S-adenosylmethionine and polyamine biosynthesis.
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Affiliation(s)
- Bartosz Sekula
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL, USA.
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL, USA; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL, USA
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