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Su Y, Michimori Y, Atomi H. Biochemical and genetic examination of two aminotransferases from the hyperthermophilic archaeon Thermococcus kodakarensis. Front Microbiol 2023; 14:1126218. [PMID: 36891395 PMCID: PMC9986279 DOI: 10.3389/fmicb.2023.1126218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/31/2023] [Indexed: 02/22/2023] Open
Abstract
The hyperthermophilic archaeon Thermococcus kodakarensis utilizes amino acids as a carbon and energy source. Multiple aminotransferases, along with glutamate dehydrogenase, are presumed to be involved in the catabolic conversion of amino acids. T. kodakarensis harbors seven Class I aminotransferase homologs on its genome. Here we examined the biochemical properties and physiological roles of two Class I aminotransferases. The TK0548 protein was produced in Escherichia coli and the TK2268 protein in T. kodakarensis. Purified TK0548 protein preferred Phe, Trp, Tyr, and His, and to a lower extent, Leu, Met and Glu. The TK2268 protein preferred Glu and Asp, with lower activities toward Cys, Leu, Ala, Met and Tyr. Both proteins recognized 2-oxoglutarate as the amino acceptor. The TK0548 protein exhibited the highest k cat/K m value toward Phe, followed by Trp, Tyr, and His. The TK2268 protein exhibited highest k cat/K m values for Glu and Asp. The TK0548 and TK2268 genes were individually disrupted, and both disruption strains displayed a retardation in growth on a minimal amino acid medium, suggesting their involvement in amino acid metabolism. Activities in the cell-free extracts of the disruption strains and the host strain were examined. The results suggested that the TK0548 protein contributes to the conversion of Trp, Tyr and His, and the TK2268 protein to that of Asp and His. Although other aminotransferases seem to contribute to the transamination of Phe, Trp, Tyr, Asp, and Glu, our results suggest that the TK0548 protein is responsible for the majority of aminotransferase activity toward His in T. kodakarensis. The genetic examination carried out in this study provides insight into the contributions of the two aminotransferases toward specific amino acids in vivo, an aspect which had not been thoroughly considered thus far.
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Affiliation(s)
- Yu Su
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.,Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
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Kristensen DB, Ørgaard M, Sloth TM, Christoffersen NS, Leth-Espensen KZ, Jensen PF. Optimized Multi-Attribute Method Workflow Addressing Missed Cleavages and Chromatographic Tailing/Carry-Over of Hydrophobic Peptides. Anal Chem 2022; 94:17195-17204. [PMID: 36346901 DOI: 10.1021/acs.analchem.2c03820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide mapping by liquid chromatography mass spectrometry (LC-MS) and the related multi-attribute method (MAM) are well-established analytical tools for verification of the primary structure and mapping/quantitation of co- and post-translational modifications (PTMs) or product quality attributes in biopharmaceutical development. Proteolytic digestion is a key step in peptide mapping workflows, which traditionally is labor-intensive, involving multiple manual steps. Recently, simple high-temperature workflows with automatic digestion were introduced, which facilitate robustness and reproducibility across laboratories. Here, a modified workflow with an automatic digestion step is presented, which includes a two-step digestion at high and low temperatures, as opposed to the original one-step digestion at a high temperature. The new automatic digestion workflow significantly reduces the number of missed cleavages, obtaining a more complete digestion profile. In addition, we describe how chromatographic peak tailing and carry-over is dramatically reduced for hydrophobic peptides by switching from the traditional C18 reversed-phase (RP) column chemistry used for peptide mapping to a less retentive C4 column chemistry. No negative impact is observed on MS/MS-derived sequence coverage when switching to a C4 column chemistry. Overall, the new peptide mapping workflow significantly reduces the number of missed cleavages, yielding more robust and simple data interpretation, while providing dramatically reduced tailing and carry-over of hydrophobic peptides.
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Aakeröy CB, Smith M, Desper J. Finding a single-molecule receptor for citramalic acid through supramolecular chelation. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have demonstrated that the tritopic hydrogen-bond acceptor 1,3,5-(5,6-dimethylbenzimidazol-1-yl)-2,4,6-trimethylbenzene can act as a perfectly complementary receptor for citramalic acid. The solid-state structure of the cocrystal of the two components show that they form 1:1 pairs where each pair is held together by three near-linear O–H···N hydrogen bonds in a converging manner. The conformational flexibility of both species is apparently no hindrance to the formation of discrete dimeric “cups” wherein each species presents three hydrogen-bond donors/acceptors in a face-to-face orientation.
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Affiliation(s)
- Christer B. Aakeröy
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
| | - Michelle Smith
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
| | - John Desper
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
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Moreno MA, Abramov A, Abendroth J, Alonso A, Zhang S, Alcolea PJ, Edwards T, Lorimer D, Myler PJ, Larraga V. Structure of tyrosine aminotransferase from Leishmania infantum. Acta Crystallogr F Struct Biol Commun 2014; 70:583-7. [PMID: 24817714 PMCID: PMC4014323 DOI: 10.1107/s2053230x14007845] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 04/08/2014] [Indexed: 11/12/2022] Open
Abstract
The trypanosomatid parasite Leishmania infantum is the causative agent of visceral leishmaniasis (VL), which is usually fatal unless treated. VL has an incidence of 0.5 million cases every year and is an important opportunistic co-infection in HIV/AIDS. Tyrosine aminotransferase (TAT) has an important role in the metabolism of trypanosomatids, catalyzing the first step in the degradation pathway of aromatic amino acids, which are ultimately converted into their corresponding L-2-oxoacids. Unlike the enzyme in Trypanosoma cruzi and mammals, L. infantum TAT (LiTAT) is not able to transaminate ketoglutarate. Here, the structure of LiTAT at 2.35 Å resolution is reported, and it is confirmed that the presence of two Leishmania-specific residues (Gln55 and Asn58) explains, at least in part, this specific reactivity. The difference in substrate specificity between leishmanial and mammalian TAT and the importance of this enzyme in parasite metabolism suggest that it may be a useful target in the development of new drugs against leishmaniasis.
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Affiliation(s)
- M. A. Moreno
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - A. Abramov
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Seattle, WA 98109, USA
| | - J. Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Emerald Bio Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - A. Alonso
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - S. Zhang
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Seattle, WA 98109, USA
| | - P. J. Alcolea
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - T. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Emerald Bio Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Emerald Bio Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - P. J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Seattle, WA 98109, USA
- Department of Global Health and Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98125, USA
| | - V. Larraga
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
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Abstract
Pyridoxal phosphate (PLP)-dependent enzymes are unrivaled in the diversity of reactions that they catalyze. New structural data have paved the way for targeted mutagenesis and mechanistic studies and have provided a framework for interpretation of those results. Together, these complementary approaches yield new insight into function, particularly in understanding the origins of substrate and reaction type specificity. The combination of new sequences and structures enables better reconstruction of their evolutionary heritage and illuminates unrecognized similarities within this diverse group of enzymes. The important metabolic roles of many PLP-dependent enzymes drive efforts to design specific inhibitors, which are now guided by the availability of comprehensive structural and functional databases. Better understanding of the function of this important group of enzymes is crucial not only for inhibitor design, but also for the design of improved protein-based catalysts.
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Affiliation(s)
- Andrew C Eliot
- Department of Chemistry University of California, Berkeley, California 94720-3206, USA.
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Venhorst J, ter Laak AM, Meijer M, van de Wetering I, Commandeur JNM, Rooseboom M, Vermeulen NPE. Modeling and molecular dynamics of glutamine transaminase K/cysteine conjugate beta-lyase. J Mol Graph Model 2003; 22:55-70. [PMID: 12798391 DOI: 10.1016/s1093-3263(03)00136-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The homodimeric, pyridoxal 5'-phosphate (PLP)-dependent enzyme glutamine transaminase K/cysteine conjugate beta-lyase (GTK/beta-lyase) has been implicated in the bioactivation of chemopreventive compounds. This paper describes the first homology model of rat renal GTK/beta-lyase and its active site residues, deduced from molecular dynamics (MD) simulations of the binding mode of 13 structurally diverse cysteine S-conjugates and amino acids after Amber-parametrization of PLP. Comparison with Thermus thermophilus aspartate aminotransferase (tAAT) and Trypanosoma cruzi tyrosine aminotransferase (tTAT), used as templates for modeling GTK/beta-lyase, showed that the PLP-binding site of GTK/beta-lyase is highly conserved. Binding of the ligand alpha-carboxylate-group occurred via the conserved residues Arg(432) and Asn(219), and Asn(50) and Gly(70). Two pockets accommodated the various ligand side chains. A small pocket, located directly above PLP, was of a highly hydrophobic and aromatic character. A larger pocket, formed partly by the substrate access channel, was more hydrophilic and notably involved the salt bridge partners Glu(54) and Arg(99*) (* denotes the other subunit). Ligand-binding residues included Leu(51), Phe(71), Tyr(135), Phe(373) and Phe(312*), and pi-stacking interactions were often observed. Tyr(135) and Asn(50) were prominent in hydrogen bonding with the sulfur-atom of cysteine S-conjugates. The observed binding mode of the ligands corresponded well with their experimentally determined inhibitory potency toward GTK/beta-lyase. The current homology model thus provides a starting point for further validation of the role of active site residues in ligand-binding by means of mutagenesis studies. Ultimately, insight in the binding of ligands to GTK/beta-lyase may result in the rational design of new ligands and selective inhibitors.
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Affiliation(s)
- Jennifer Venhorst
- Department of Pharmacochemistry, Division of Molecular Toxicology, Leiden/Amsterdam Center for Drug Research (LACDR), Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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Goto M, Omi R, Miyahara I, Sugahara M, Hirotsu K. Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction. J Biol Chem 2003; 278:22964-71. [PMID: 12684518 DOI: 10.1074/jbc.m213198200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Argininosuccinate synthetase reversibly catalyzes the ATP-dependent condensation of a citrulline with an aspartate to give argininosuccinate. The structures of the enzyme from Thermus thermophilus HB8 complexed with intact ATP and substrates (citrulline and aspartate) and with AMP and product (argininosuccinate) have been determined at 2.1- and 2.0-A resolution, respectively. The enzyme does not show the ATP-induced domain rotation observed in the enzyme from Escherichia coli. In the enzyme-substrate complex, the reaction sites of ATP and the bound substrates are adjacent and are sufficiently close for the reaction to proceed without the large conformational change at the domain level. The mobility of the triphosphate group in ATP and the side chain of citrulline play an important role in the catalytic action. The protonated amino group of the bound aspartate interacts with the alpha-phosphate of ATP and the ureido group of citrulline, thus stimulating the adenylation of citrulline. The enzyme-product complex explains how the citrullyl-AMP intermediate is bound to the active site. The stereochemistry of the catalysis of the enzyme is clarified on the basis of the structures of tAsS (argininosuccinate synthetase from T. thermophilus HB8) complexes.
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Affiliation(s)
- Masaru Goto
- Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan
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Denesyuk AI, Denessiouk KA, Korpela T, Johnson MS. Phosphate group binding "cup" of PLP-dependent and non-PLP-dependent enzymes: leitmotif and variations. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1647:234-8. [PMID: 12686139 DOI: 10.1016/s1570-9639(03)00057-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Pyridoxal-5'-phosphate (PLP) is widely used by many enzymes in reactions where amino acids are interconverted. Whereas the role of the pyridoxal ring in catalysis is well understood, the functional role of the single phosphate group in PLP has been less studied. Here we construct unambiguous connection diagrams that describe the interactions among the three non-ester phosphate oxygen atoms of PLP and surrounding atoms from the protein binding site and from water molecules, the so-called phosphate group binding "cup". These diagrams provide a simple means to identify common recognition motifs for the phosphate group in both similar and different protein folds. Diagrams were constructed and compared in the cases of five newly determined structures of PLP-dependent transferases (fold type I enzymes) and, additionally, two non-PLP protein complexes (indole-3-glycerol phosphate synthase (IGPS) with bound indole-3-glycerol phosphate (IGP) and old yellow enzyme (OYE) with bound flavin mononucleotide (FMN)). A detailed comparison of the diagrams shows that three positions out of ten in the structure of the phosphate group binding "cup" contain invariant atoms, while seven others are occupied by conserved atom types. This level of similarity was also observed in the fold type III (TIM beta/alpha-barrel) enzymes that bind three different ligands: PLP, IGP and FMN.
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Affiliation(s)
- Alexander I Denesyuk
- Department of Biochemistry and Pharmacy, Abo Akademi University, Tykistökatu 6A, FIN-20521 Turku, Finland
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