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1.
Int J Biol Macromol ; 267(Pt 1): 131326, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38569988

RESUMO

Aspartate kinase (AK), an enzyme from the Wolbachia endosymbiont of Brugia malayi (WBm), plays a pivotal role in the bacterial cell wall and amino acid biosynthesis, rendering it an attractive candidate for therapeutic intervention. Allosteric inhibition of aspartate kinase is a prevalent mode of regulation across microorganisms and plants, often modulated by end products such as lysine, threonine, methionine, or meso-diaminopimelate. The intricate and diverse nature of microbial allosteric regulation underscores the need for rigorous investigation. This study employs a combined experimental and computational approach to decipher the allosteric regulation of WBmAK. Molecular Dynamics (MD) simulations elucidate that ATP (cofactor) and ASP (substrate) binding induce a closed conformation, promoting enzymatic activity. In contrast, the binding of lysine (allosteric inhibitor) leads to enzyme inactivation and an open conformation. The enzymatic assay demonstrates the optimal activity of WBmAK at 28 °C and a pH of 8.0. Notably, the allosteric inhibition study highlights lysine as a more potent inhibitor compared to threonine. Importantly, this investigation sheds light on the allosteric mechanism governing WBmAK and imparts novel insights into structure-based drug discovery, paving the way for the development of effective inhibitors against filarial pathogens.


Assuntos
Aspartato Quinase , Brugia Malayi , Simulação de Dinâmica Molecular , Wolbachia , Brugia Malayi/enzimologia , Brugia Malayi/microbiologia , Regulação Alostérica , Animais , Aspartato Quinase/metabolismo , Aspartato Quinase/genética , Aspartato Quinase/química , Simbiose , Trifosfato de Adenosina/metabolismo , Lisina/química , Lisina/metabolismo
2.
Appl Environ Microbiol ; 90(4): e0015524, 2024 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-38456673

RESUMO

Humans and mammals need to ingest essential amino acids (EAAs) for protein synthesis. In addition to their importance as nutrients, EAAs are involved in brain homeostasis. However, elderly people are unable to efficiently consume EAAs from their daily diet due to reduced appetite and variations in the contents of EAAs in foods. On the other hand, strains of the yeast Saccharomyces cerevisiae that accumulate EAAs would enable elderly people to intakegest adequate amounts of EAAs and thus might slow down the neurodegenerative process, contributing to the extension of their healthy lifespan. In this study, we isolated a mutant (strain HNV-5) that accumulates threonine, an EAA, derived from a diploid laboratory yeast by conventional mutagenesis. Strain HNV-5 carries a novel mutation in the HOM3 gene encoding the Ala462Thr variant of aspartate kinase (AK). Enzymatic analysis revealed that the Ala462Thr substitution significantly decreased the sensitivity of AK activity to threonine feedback inhibition even in the presence of 50 mM threonine. Interestingly, Ala462Thr substitution did not affect the catalytic ability of Hom3, in contrast to previously reported amino acid substitutions that resulted in reduced sensitivity to threonine feedback inhibition. Furthermore, yeast cells expressing the Ala462Thr variant showed an approximately threefold increase in intracellular threonine content compared to that of the wild-type Hom3. These findings will be useful for the development of threonine-accumulating yeast strains that may improve the quality of life in elderly people.IMPORTANCEFor humans and mammals, essential amino acids (EAAs) play an important role in maintaining brain function. Therefore, increasing the intake of EAAs by using strains of the yeast Saccharomyces cerevisiae that accumulate EAAs may inhibit neurodegeneration in elderly people and thus contribute to extending healthy lifespan and improving their quality of life. Threonine, an EAA, is synthesized from aspartate. Aspartate kinase (AK) catalyzes the first step in threonine biosynthesis and is subject to allosteric regulation by threonine. Here, we isolated a threonine-accumulating mutant of S. cerevisiae by conventional mutagenesis and identified a mutant gene encoding a novel variant of AK. In contrast to previously isolated variants, the Hom3 variant exhibited AK activity that was insensitive to feedback inhibition by threonine but retained its catalytic ability. This resulted in increased production of threonine in yeast. These findings open up the possibility for the rational design of AK to increase threonine productivity in yeast.


Assuntos
Aspartato Quinase , Saccharomyces cerevisiae , Humanos , Animais , Idoso , Saccharomyces cerevisiae/metabolismo , Treonina , Aspartato Quinase/química , Aspartato Quinase/genética , Aspartato Quinase/metabolismo , Retroalimentação , Qualidade de Vida , Mamíferos
3.
Molecules ; 26(2)2021 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-33477510

RESUMO

The serine biosynthetic pathway is a key element contributing to tumor proliferation. In recent years, targeting of phosphoglycerate dehydrogenase (PHGDH), the first enzyme of this pathway, intensified and revealed to be a promising strategy to develop new anticancer drugs. Among attractive PHGDH inhibitors are the α-ketothioamides. In previous work, we have demonstrated their efficacy in the inhibition of PHGDH in vitro and in cellulo. However, the precise site of action of this series, which would help the rational design of new inhibitors, remained undefined. In the present study, the detailed mechanism-of-action of a representative α-ketothioamide inhibitor is reported using several complementary experimental techniques. Strikingly, our work led to the identification of an allosteric site on PHGDH that can be targeted for drug development. Using mass spectrometry experiments and an original α-ketothioamide diazirine-based photoaffinity probe, we identified the 523Q-533F sequence on the ACT regulatory domain of PHGDH as the binding site of α-ketothioamides. Mutagenesis experiments further documented the specificity of our compound at this allosteric site. Our results thus pave the way for the development of new anticancer drugs using a completely novel mechanism-of-action.


Assuntos
Diazometano/química , Inibidores Enzimáticos/farmacologia , Espectrometria de Massas/métodos , Fosfoglicerato Desidrogenase/antagonistas & inibidores , Fosfoglicerato Desidrogenase/metabolismo , Sítio Alostérico , Aspartato Quinase/química , Aspartato Quinase/metabolismo , Sítios de Ligação , Corismato Mutase/química , Corismato Mutase/metabolismo , Humanos , Estrutura Molecular , Domínios Proteicos , Relação Estrutura-Atividade
4.
FEBS J ; 288(7): 2377-2397, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33067840

RESUMO

The stringent response, regulated by the bifunctional (p)ppGpp synthetase/hydrolase Rel in mycobacteria, is critical for long-term survival of the drug-tolerant dormant state of Mycobacterium tuberculosis. During amino acid starvation, MtRel senses a drop in amino acid concentration and synthesizes the messengers pppGpp and ppGpp, collectively called (p)ppGpp. Here, we investigate the role of the regulatory 'Aspartokinase, Chorismate mutase and TyrA' (ACT) domain in MtRel. Using NMR spectroscopy approaches, we report the high-resolution structure of dimeric MtRel ACT which selectively binds to valine out of all other branched-chain amino acids tested. A set of MtRel ACT mutants were generated to identify the residues required for maintaining the head-to-tail dimer. Through NMR titrations, we determined the crucial residues for binding of valine and show structural rearrangement of the MtRel ACT dimer in the presence of valine. This study suggests the direct involvement of amino acids in (p)ppGpp accumulation mediated by MtRel independent to interactions with stalled ribosomes. Database Structural data are available in the PDB database under the accession number 6LXG.


Assuntos
Aspartato Quinase/genética , Corismato Mutase/genética , Ligases/genética , Mycobacterium tuberculosis/genética , Aspartato Quinase/química , Aspartato Quinase/ultraestrutura , Corismato Mutase/química , Corismato Mutase/ultraestrutura , Guanosina Tetrafosfato/genética , Hidrolases/genética , Ligases/química , Ligases/ultraestrutura , Espectroscopia de Ressonância Magnética , Mycobacterium tuberculosis/patogenicidade , Domínios Proteicos/genética , Multimerização Proteica , Fatores de Transcrição/genética
5.
Amino Acids ; 52(4): 649-666, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32306102

RESUMO

Amino acid metabolic enzymes often contain a regulatory ACT domain, named for aspartate kinase, chorismate mutase, and TyrA (prephenate dehydrogenase). Arabidopsis encodes 12 putative amino acid sensor ACT repeat (ACR) proteins, all containing ACT repeats but no identifiable catalytic domain. Arabidopsis ACRs comprise three groups based on domain composition and sequence: group I and II ACRs contain four ACTs each, and group III ACRs contain two ACTs. Previously, all three groups had been documented only in Arabidopsis. Here, we extended this to algae and land plants, showing that all three groups of ACRs are present in most, if not all, land plants, whereas among algal ACRs, although quite diverse, only group III is conserved. The appearance of canonical group I and II ACRs thus accompanied the evolution of plants from living in water to living on land. Alignment of ACTs from plant ACRs revealed a conserved motif, DRPGLL, at the putative ligand-binding site. Notably, the unique features of the DRPGLL motifs in each ACT domain are conserved in ACRs from algae to land plants. The conservation of plant ACRs is reminiscent of that of human cellular arginine sensor for mTORC1 (CASTOR1), a member of a small protein family highly conserved in animals. CASTOR proteins also have four ACT domains, although the sequence identities between ACRs and CASTORs are very low. Thus, plant ACRs and animal CASTORs may have adapted the regulatory ACT domains from a more ancient metabolic enzyme, and then evolved independently.


Assuntos
Aminoácidos/metabolismo , Aspartato Quinase/classificação , Corismato Mutase/classificação , Evolução Molecular , Oryza/enzimologia , Proteínas de Plantas/classificação , Prefenato Desidrogenase/classificação , Motivos de Aminoácidos , Arabidopsis/enzimologia , Aspartato Quinase/química , Clorófitas/enzimologia , Corismato Mutase/química , Sequência Conservada , Filogenia , Proteínas de Plantas/química , Prefenato Desidrogenase/química , Domínios Proteicos , Rodófitas/enzimologia
6.
Biochem J ; 475(6): 1107-1119, 2018 03 20.
Artigo em Inglês | MEDLINE | ID: mdl-29382741

RESUMO

In plants and microorganisms, aspartate kinase (AK) catalyzes an initial commitment step of the aspartate family amino acid biosynthesis. Owing to various structural organizations, AKs from different species show tremendous diversity and complex allosteric controls. We report the crystal structure of AK from Pseudomonas aeruginosa (PaAK), a typical α2ß2 hetero-tetrameric enzyme, in complex with inhibitory effectors. Distinctive features of PaAK are revealed by structural and biochemical analyses. Essentially, the open conformation of Lys-/Thr-bound PaAK structure clarifies the inhibitory mechanism of α2ß2-type AK. Moreover, the various inhibitory effectors of PaAK have been identified and a general amino acid effector motif of AK family is described.


Assuntos
Aspartato Quinase/química , Aspartato Quinase/metabolismo , Pseudomonas aeruginosa/enzimologia , Regulação Alostérica/genética , Sítio Alostérico/genética , Sequência de Aminoácidos , Aspartato Quinase/genética , Catálise , Modelos Moleculares , Organismos Geneticamente Modificados , Domínios e Motivos de Interação entre Proteínas/genética , Pseudomonas aeruginosa/genética , Alinhamento de Sequência
7.
Nature ; 536(7615): 229-33, 2016 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-27487210

RESUMO

The mechanistic Target of Rapamycin Complex 1 (mTORC1) is a major regulator of eukaryotic growth that coordinates anabolic and catabolic cellular processes with inputs such as growth factors and nutrients, including amino acids. In mammals arginine is particularly important, promoting diverse physiological effects such as immune cell activation, insulin secretion, and muscle growth, largely mediated through activation of mTORC1 (refs 4, 5, 6, 7). Arginine activates mTORC1 upstream of the Rag family of GTPases, through either the lysosomal amino acid transporter SLC38A9 or the GATOR2-interacting Cellular Arginine Sensor for mTORC1 (CASTOR1). However, the mechanism by which the mTORC1 pathway detects and transmits this arginine signal has been elusive. Here, we present the 1.8 Å crystal structure of arginine-bound CASTOR1. Homodimeric CASTOR1 binds arginine at the interface of two Aspartate kinase, Chorismate mutase, TyrA (ACT) domains, enabling allosteric control of the adjacent GATOR2-binding site to trigger dissociation from GATOR2 and downstream activation of mTORC1. Our data reveal that CASTOR1 shares substantial structural homology with the lysine-binding regulatory domain of prokaryotic aspartate kinases, suggesting that the mTORC1 pathway exploited an ancient, amino-acid-dependent allosteric mechanism to acquire arginine sensitivity. Together, these results establish a structural basis for arginine sensing by the mTORC1 pathway and provide insights into the evolution of a mammalian nutrient sensor.


Assuntos
Arginina/metabolismo , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Complexos Multiproteicos/metabolismo , Serina-Treonina Quinases TOR/metabolismo , Regulação Alostérica/efeitos dos fármacos , Sítio Alostérico/efeitos dos fármacos , Arginina/química , Arginina/deficiência , Arginina/farmacologia , Aspartato Quinase/química , Aspartato Quinase/metabolismo , Cristalografia por Raios X , Ativação Enzimática/efeitos dos fármacos , Evolução Molecular , Humanos , Peptídeos e Proteínas de Sinalização Intracelular , Lisina/metabolismo , Alvo Mecanístico do Complexo 1 de Rapamicina , Modelos Moleculares , Complexos Multiproteicos/química , Ligação Proteica/efeitos dos fármacos , Multimerização Proteica , Estrutura Terciária de Proteína , Transdução de Sinais/efeitos dos fármacos , Serina-Treonina Quinases TOR/química
8.
Extremophiles ; 20(3): 275-82, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-26936147

RESUMO

TTHA0829 from Thermus thermophilus HB8 has a molecular mass of 22,754 Da and is composed of 210 amino acid residues. The expression of TTHA0829 is remarkably elevated in the latter half of logarithmic growth phase. TTHA0829 can form either a tetrameric or dimeric structure, and main-chain folding provides an N-terminal cystathionine-ß-synthase (CBS) domain and a C-terminal aspartate-kinase chorismate-mutase tyrA (ACT) domain. Both CBS and ACT are regulatory domains to which a small ligand molecule can bind. The CBS domain is found in proteins from organisms belonging to all kingdoms and is observed frequently as two or four tandem copies. This domain is considered as a small intracellular module with a regulatory function and is typically found adjacent to the active (or functional) site of several enzymes and integral membrane proteins. The ACT domain comprises four ß-strands and two α-helices in a ßαßßαß motif typical of intracellular small molecule binding domains that help control metabolism, solute transport and signal transduction. We discuss the possible role of TTHA0829 based on its structure and expression pattern. The results imply that TTHA0829 acts as a cell-stress sensor or a metabolite acceptor.


Assuntos
Aspartato Quinase/química , Proteínas de Bactérias/química , Corismato Mutase/química , Cistationina beta-Sintase/química , Thermus thermophilus/genética , Aspartato Quinase/genética , Aspartato Quinase/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Corismato Mutase/genética , Corismato Mutase/metabolismo , Cistationina beta-Sintase/genética , Cistationina beta-Sintase/metabolismo , Domínios Proteicos , Thermus thermophilus/enzimologia
9.
Int J Mol Sci ; 16(12): 28270-84, 2015 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-26633359

RESUMO

Aspartate kinase (AK) is the key enzyme in the biosynthesis of aspartate-derived amino acids. Recombinant AK was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. Homogeneous AK was predicted as a decamer with a molecular weight of ~48 kDa and a half-life of 4.5 h. The enzymatic activity was enhanced by ethanol and Ni(2+). Moreover, steady-state kinetic study confirmed that AK is an allosteric enzyme, and its activity was inhibited by allosteric inhibitors, such as Lys, Met, and Thr. Theoretical results indicated the binding mode of AK and showed that Arg169 is an important residue in substrate binding, catalytic domain, and inhibitor binding. The values of the kinetic parameter Vmax of R169 mutants, namely, R169Y, R169P, R169D, and R169H AK, with l-aspartate as the substrate, were 4.71-, 2.25-, 2.57-, and 2.13-fold higher, respectively, than that of the wild-type AK. Furthermore, experimental and theoretical data showed that Arg169 formed a hydrogen bond with Glu92, which functions as the entrance gate. This study provides a basis to develop new enzymes and elucidate the corresponding amino acid production.


Assuntos
Aspartato Quinase/química , Domínio Catalítico , Corynebacterium/enzimologia , Modelos Moleculares , Conformação Proteica , Sequência de Aminoácidos , Aspartato Quinase/antagonistas & inibidores , Aspartato Quinase/genética , Sítios de Ligação , Corynebacterium/genética , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Dados de Sequência Molecular , Mutação , Proteínas Recombinantes , Alinhamento de Sequência , Solventes , Termodinâmica
10.
J Biomol Struct Dyn ; 33(1): 134-46, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-24279729

RESUMO

Dynamic intersubunit interactions are key elements in the regulation of many biological systems. A better understanding of how subunits interact with each other and how their interactions are related to dynamic protein structure is a fundamental task in biology. In this paper, a heteromultimeric allosteric protein, Corynebacterium glutamicum aspartokinase, is used as a model system to explore the signal transduction involved in intersubunit interactions and allosteric communication with an emphasis on the intersubunit signaling process. For this purpose, energy dissipation simulation and network construction are conducted for each subunit and the whole protein. Comparison with experimental results shows that the new approach is able to predict all the mutation sites that have been experimentally proved to desensitize allosteric regulation of the enzyme. Additionally, analysis revealed that the function of the effector threonine is to facilitate the binding of the two subunits without contributing to the allosteric communication. During the allosteric regulation upon the binding of the effector lysine, signals can be transferred from the ß-subunit to the catalytic site of the α-subunit through both a direct way of intersubunit signal transduction, and an indirect way: first, to the regulatory region of the α-subunit by intersubunit signal transduction and then to the catalytic region by intramolecular signal transduction. Therefore, the new approach is able to illustrate the diversity of the underlying mechanisms when the strength of feedback inhibition by the effector(s) is modulated, providing useful information that has potential applications in engineering heteromultimeric allosteric regulation.


Assuntos
Aspartato Quinase/química , Proteínas de Bactérias/química , Transdução de Sinais , Termodinâmica , Algoritmos , Aspartato Quinase/genética , Aspartato Quinase/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Corynebacterium glutamicum/enzimologia , Corynebacterium glutamicum/genética , Lisina/química , Lisina/genética , Lisina/metabolismo , Simulação de Dinâmica Molecular , Mutação , Ligação Proteica , Multimerização Proteica , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Subunidades Proteicas/química , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Treonina/química , Treonina/genética , Treonina/metabolismo
11.
Wei Sheng Wu Xue Bao ; 54(6): 663-9, 2014 Jun 04.
Artigo em Chinês | MEDLINE | ID: mdl-25272815

RESUMO

OBJECTIVE: Increasing the activity of aspartokinase (AK) from Corynebacterium pekinense. METHODS: The gene of AK was constructed and mutated by site-specific mutagenesis. The mutational recombinant plasmid was heterologously expressed in Escherichia coli BL21. The mutational AK was purified by Ni(2+)-NTA column after ultrasonicating of the recombinant bacteria, and then identified by SDS-PAGE and Western blot. We compared the kinetic difference between R169H AK and WT AK by determining the enzymatic activities. Some other characteristics of R169H AK and WTAK were also studied. RESULTS: The mutant R169H was successfully constructed. The molecular weight of AK was 48kDa. V(max) of R169H AK was 226.3 U/mg x s(-1), which was 2.3 times higher than that of WT AK. The optimum reaction temperature of R169H AK was 26 degrees C, the same as that of WT AK. The optimum reaction pH of R169H AK was 9.0, slightly higher than that of WT AK. The half-life period of R169H AK under optimum temperature and pH were 5.5h, much higher than that of WT AK. Lysine, threonine and methionine had an active effect on the activity of R169H AK when they were in low concentration. CONCLUSION: The hydrogen bond between R169 and E92 was broken down in R169H AK, which could affect the degree of polymerization and further lowered the affinity of mutant AK with substrates and then decreased the inhibition inducing by the metabolites. Thus, the V(max) of mutant AK from R169H had increased by 2.3 times compared with that of WT AK.


Assuntos
Aspartato Quinase/química , Aspartato Quinase/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Corynebacterium/enzimologia , Mutação de Sentido Incorreto , Aspartato Quinase/metabolismo , Proteínas de Bactérias/metabolismo , Corynebacterium/química , Corynebacterium/genética , Estabilidade Enzimática , Cinética , Modelos Moleculares
12.
Physiol Plant ; 149(2): 188-99, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-23330606

RESUMO

In poplar, we identified proteins homologous to yeast proteins involved in osmosensing multistep phosphorelay Sln1p-Ypd1p-Ssk1p. This finding led us to speculate that Populus cells could sense osmotic stress by a similar mechanism. This study focuses on first and second protagonists of this possible pathway: a histidine-aspartate kinase (HK1), putative osmosensor and histidine phosphotransfer proteins (HPt1 to 10), potential partners of this HK. Characterization of HK1 showed its ability to homodimerize in two-hybrid tests and to act as an osmosensor with a kinase activity in yeast, by functional complementation of sln1Δ sho1Δ strain. Moreover, in plant cells, plasma membrane localization of HK1 is shown. Further analysis on HPts allowed us to isolate seven new cDNAs, leading to a total of 10 different HPts identified in poplar. Interaction tests showed that almost all HPts can interact with HK1, but two of them exhibit stronger interactions, suggesting a preferential partnership in poplar. The importance of the phosphorylation status in these interactions has been investigated with two-hybrid tests carried out with mutated HK1 forms. Finally, in planta co-expression analysis of genes encoding these potential partners revealed that only three HPts are co-expressed with HK1 in different poplar organs. This result reinforces the hypothesis of a partnership between HK1 and these three preferential HPts in planta. Taken together, these results shed some light on proteins partnerships that could be involved in the osmosensing pathway in Populus.


Assuntos
Aspartato Quinase/metabolismo , Histidina/metabolismo , Proteínas de Plantas/metabolismo , Populus/metabolismo , Proteínas Quinases/metabolismo , Sequência de Aminoácidos , Aspartato Quinase/química , Aspartato Quinase/genética , Western Blotting , Teste de Complementação Genética , Histidina/genética , Histidina Quinase , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Dados de Sequência Molecular , Mutação , Fosforilação , Proteínas de Plantas/química , Proteínas de Plantas/genética , Populus/genética , Ligação Proteica , Proteínas Quinases/química , Proteínas Quinases/genética , Multimerização Proteica , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crescimento & desenvolvimento , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Homologia de Sequência de Aminoácidos , Técnicas do Sistema de Duplo-Híbrido
13.
Subcell Biochem ; 64: 283-302, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23080256

RESUMO

L-threonine, one of the three major amino acids produced throughout the world, has a wide application in industry, as an additive or as a precursor for the biosynthesis of other chemicals. It is predominantly produced through microbial fermentation the efficiency of which largely depends on the quality of strains. Metabolic engineering based on a cogent understanding of the metabolic pathways of L-threonine biosynthesis and regulation provides an effective alternative to the traditional breeding for strain development. Continuing efforts have been made in revealing the mechanisms and regulation of L-threonine producing strains, as well as in metabolic engineering of suitable organisms whereby genetically-defined, industrially competitive L-threonine producing strains have been successfully constructed. This review focuses on the global metabolic and regulatory networks responsible for L-threonine biosynthesis, the molecular mechanisms of regulation, and the strategies employed in strain engineering.


Assuntos
Corynebacterium glutamicum/metabolismo , Escherichia coli/metabolismo , Engenharia Metabólica/métodos , Treonina/biossíntese , Aspartato Quinase/química , Aspartato Quinase/genética , Aspartato Quinase/metabolismo , Carbono/metabolismo , Corynebacterium glutamicum/genética , Escherichia coli/genética , Regulação Bacteriana da Expressão Gênica , Redes e Vias Metabólicas/genética , Modelos Moleculares
14.
PLoS One ; 7(2): e31529, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22363664

RESUMO

A novel approach to reveal intramolecular signal transduction network is proposed in this work. To this end, a new algorithm of network construction is developed, which is based on a new protein dynamics model of energy dissipation. A key feature of this approach is that direction information is specified after inferring protein residue-residue interaction network involved in the process of signal transduction. This enables fundamental analysis of the regulation hierarchy and identification of regulation hubs of the signaling network. A well-studied allosteric enzyme, E. coli aspartokinase III, is used as a model system to demonstrate the new method. Comparison with experimental results shows that the new approach is able to predict all the sites that have been experimentally proved to desensitize allosteric regulation of the enzyme. In addition, the signal transduction network shows a clear preference for specific structural regions, secondary structural types and residue conservation. Occurrence of super-hubs in the network indicates that allosteric regulation tends to gather residues with high connection ability to collectively facilitate the signaling process. Furthermore, a new parameter of propagation coefficient is defined to determine the propagation capability of residues within a signal transduction network. In conclusion, the new approach is useful for fundamental understanding of the process of intramolecular signal transduction and thus has significant impact on rational design of novel allosteric proteins.


Assuntos
Aspartato Quinase/metabolismo , Escherichia coli/enzimologia , Transdução de Sinais , Algoritmos , Motivos de Aminoácidos , Aminoácidos/metabolismo , Aspartato Quinase/química , Modelos Moleculares , Simulação de Dinâmica Molecular , Mutação/genética , Conformação Proteica , Termodinâmica
15.
Arch Biochem Biophys ; 519(2): 186-93, 2012 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-22079167

RESUMO

Based on recent X-ray structures and biochemical characterizations of aspartate kinases from different species, we show in this review how various organizations of a regulatory domain have contributed to the different mechanisms of control observed in aspartate kinases allowing simple to complex allosteric controls in branched pathways. The aim of this review is to show the relationships between domain organization, effector binding sites, mechanism of inhibition and regulatory function of an allosteric enzyme in a biosynthetic pathway.


Assuntos
Aspartato Quinase , Regulação Alostérica , Aspartato Quinase/química , Aspartato Quinase/metabolismo , Sítios de Ligação , Cinética , Estrutura Terciária de Proteína
16.
Protein Cell ; 2(9): 745-54, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21976064

RESUMO

The aspartate kinase (AK) from Mycobacterium tuberculosis (Mtb) catalyzes the biosynthesis of aspartate family amino acids, including lysine, threonine, isoleucine and methionine. We determined the crystal structures of the regulatory subunit of aspartate kinase from Mtb alone (referred to as MtbAKß) and in complex with threonine (referred to as MtbAKß-Thr) at resolutions of 2.6 Å and 2.0 Å, respectively. MtbAKß is composed of two perpendicular non-equivalent ACT domains [aspartate kinase, chorismate mutase, and TyrA (prephenate dehydrogenase)] per monomer. Each ACT domain contains two α helices and four antiparallel ß strands. The structure of MtbAKß shares high similarity with the regulatory subunit of the aspartate kinase from Corynebacterium glutamicum (referred to as CgAKß), suggesting similar regulatory mechanisms. Biochemical assays in our study showed that MtbAK is inhibited by threonine. Based on crystal structure analysis, we discuss the regulatory mechanism of MtbAK.


Assuntos
Aspartato Quinase/química , Mycobacterium tuberculosis/enzimologia , Treonina/metabolismo , Sequência de Aminoácidos , Aspartato Quinase/genética , Aspartato Quinase/metabolismo , Sítios de Ligação , Clonagem Molecular , Corynebacterium glutamicum/enzimologia , Cristalização/métodos , Cristalografia por Raios X , Ativação Enzimática , Ensaios Enzimáticos , Escherichia coli/genética , Escherichia coli/metabolismo , Vetores Genéticos/genética , Vetores Genéticos/metabolismo , Lisina/farmacologia , Dados de Sequência Molecular , Mycobacterium tuberculosis/efeitos dos fármacos , Plasmídeos/genética , Plasmídeos/metabolismo , Prefenato Desidrogenase/metabolismo , Estrutura Secundária de Proteína , Treonina/farmacologia
17.
PLoS One ; 6(10): e26453, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-22022616

RESUMO

Protein dynamics is essential for its function, especially for intramolecular signal transduction. In this work we propose a new concept, energy dissipation model, to systematically reveal protein dynamics upon effector binding and energy perturbation. The concept is applied to better understand the intramolecular signal transduction during allostery of enzymes. The E. coli allosteric enzyme, aspartokinase III, is used as a model system and special molecular dynamics simulations are designed and carried out. Computational results indicate that the number of residues affected by external energy perturbation (i.e. caused by a ligand binding) during the energy dissipation process shows a sigmoid pattern. Using the two-state Boltzmann equation, we define two parameters, the half response time and the dissipation rate constant, which can be used to well characterize the energy dissipation process. For the allostery of aspartokinase III, the residue response time indicates that besides the ACT2 signal transduction pathway, there is another pathway between the regulatory site and the catalytic site, which is suggested to be the ß15-αK loop of ACT1. We further introduce the term "protein dynamical modules" based on the residue response time. Different from the protein structural modules which merely provide information about the structural stability of proteins, protein dynamical modules could reveal protein characteristics from the perspective of dynamics. Finally, the energy dissipation model is applied to investigate E. coli aspartokinase III mutations to better understand the desensitization of product feedback inhibition via allostery. In conclusion, the new concept proposed in this paper gives a novel holistic view of protein dynamics, a key question in biology with high impacts for both biotechnology and biomedicine.


Assuntos
Aspartato Quinase/metabolismo , Escherichia coli/enzimologia , Modelos Moleculares , Aminoácidos/metabolismo , Aspartato Quinase/química , Domínio Catalítico , Evolução Molecular , Simulação de Dinâmica Molecular , Mutação/genética , Termodinâmica , Fatores de Tempo
18.
J Biotechnol ; 154(4): 248-54, 2011 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-21609739

RESUMO

Deregulation of allosteric inhibition of enzymes is a challenge for strain engineering and has been achieved so far primarily by random mutation and trial-and-error. In this work, we used aspartokinase, an important allosteric enzyme for industrial amino acids production, to demonstrate a predictive approach that combines protein dynamics and evolution for a rational reengineering of enzyme allostery. Molecular dynamic simulation of aspartokinase III (AK3) from Escherichia coli and statistical coupling analysis of protein sequences of the aspartokinase family allowed to identify a cluster of residues which are correlated during protein motion and coupled during the evolution. This cluster of residues forms an interconnected network mediating the allosteric regulation, including most of the previously reported positions mutated in feedback insensitive AK3 mutants. Beyond these mutation positions, we have successfully constructed another twelve targeted mutations of AK3 desensitized toward lysine inhibition. Six threonine-insensitive mutants of aspartokinase I-homoserine dehydrogenase I (AK1-HD1) were also created based on the predictions. The proposed approach can be widely applied for the deregulation of other allosteric enzymes.


Assuntos
Aminoácidos/metabolismo , Aspartato Quinase/química , Aspartato Quinase/metabolismo , Simulação de Dinâmica Molecular , Regulação Alostérica , Estrutura Secundária de Proteína
19.
Artigo em Inglês | MEDLINE | ID: mdl-21393848

RESUMO

The regulatory domain of Mycobacterium tuberculosis aspartokinase (Mtb-AK, Mtb-Ask, Rv3709c) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Screening for initial crystallization conditions using the regulatory domain (AK-ß) in the presence of the potential feedback inhibitor threonine identified four conditions which yielded crystals suitable for X-ray diffraction analysis. From these four conditions five different crystal forms of Mtb-AK-ß resulted, three of which belonged to the orthorhombic system, one to the tetragonal system and one to the monoclinic system. The highest resolution (1.6 Å) was observed for a crystal form belonging to space group P2(1)2(1)2(1), with unit-cell parameters a=53.70, b=63.43, c=108.85 Šand two molecules per asymmetric unit.


Assuntos
Aspartato Quinase/química , Aspartato Quinase/isolamento & purificação , Proteínas de Bactérias/química , Proteínas de Bactérias/isolamento & purificação , Mycobacterium tuberculosis/enzimologia , Aspartato Quinase/genética , Proteínas de Bactérias/genética , Clonagem Molecular , Cristalização , Cristalografia por Raios X , Dados de Sequência Molecular
20.
Plant Biotechnol J ; 9(2): 193-204, 2011 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-20633240

RESUMO

Threonine (Thr) is one of a few limiting essential amino acids (EAAs) in the animal feed industry, and its level in feed rations can impact production of important meat sources, such as swine and poultry. Threonine as well as EAAs lysine (Lys) and methionine (Met) are all synthesized via the aspartate family pathway. Here, we report a successful strategy to produce high free threonine soybean seed via identification of a feedback-resistant aspartate kinase (AK) enzyme that can be over-expressed in developing soybean seed. Towards this goal, we have purified and biochemically characterized AK from the enteric bacterium Xenorhabdus bovienii (Xb). Site-directed mutagenesis of XbAK identified two key regulatory residues Glu-257 and Thr-359 involved in lysine inhibition. Three feedback-resistant alleles, XbAK_T359I, XbAK_E257K and XbAK_E257K/T359I, have been generated. This study is the first to kinetically characterize the XbAK enzyme and provide biochemical and transgenic evidence that Glu-257 near the catalytic site is a critical residue for the allosteric regulation of AK. Furthermore, seed-specific expression of the feedback-resistant XbAK_T359I or XbAK_E257K allele results in increases of free Thr levels of up to 100-fold in R(1) soybean seed when compared to wild-type. Expression of feedback-sensitive wild-type AK did not substantially impact seed Thr content. In addition to high Thr, transgenic seed also showed substantial increases in other major free amino acid (FAA) levels, resulting in an up to 3.5-fold increase in the total FAA content. The transgenic seed was normal in appearance and germinated well under greenhouse conditions.


Assuntos
Aspartato Quinase/genética , Glycine max/genética , Engenharia de Proteínas/métodos , Sementes/genética , Treonina/metabolismo , Xenorhabdus/enzimologia , Aminoácidos/metabolismo , Ração Animal , Aspartato Quinase/química , Aspartato Quinase/metabolismo , Retroalimentação Fisiológica , Alimentos Geneticamente Modificados , Lisina/metabolismo , Mutagênese Sítio-Dirigida , Plantas Geneticamente Modificadas/metabolismo , Sementes/anatomia & histologia , Sementes/crescimento & desenvolvimento , Glycine max/anatomia & histologia , Glycine max/crescimento & desenvolvimento , Xenorhabdus/genética
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