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1.
Biomolecules ; 14(6)2024 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-38927089

RESUMO

Amino acid deprivation therapy (AADT) is a novel anticancer therapy, considered nontoxic and selective. Thermophilic L-asparaginase enzymes display high stability and activity at elevated temperatures. However, they are of limited use in clinical applications because of their low substrate affinity and reduced activity under physiological conditions, which may necessitate an improved dosage, leading to side effects and greater costs. Thus, in an attempt to improve the activity of L-Asn at 37 °C, with the use of a semi-rational design, eight active-site mutants of Thermococcus litoralis DSM 5473 L-asparaginase Tli10209 were developed. T70A exhibited a 5.11-fold increase compared with the wild enzyme in physiological conditions. Double-mutant enzymes were created by combining mutants with higher hydrolysis activity. T70A/F36Y, T70A/K48L, and T70A/D50G were enhanced by 5.59-, 6.38-, and 5.58-fold. The immobilized enzyme applied in MCF-7 breast cancer cells only required one-seventh of the dose of the free enzyme to achieve the same inhibition rate under near-infrared irradiation. This provides a proof of concept that it is possible to reduce the consumption of L-Asn by improving its activity, thus providing a method to manage side effects.


Assuntos
Antineoplásicos , Asparaginase , Mutagênese Sítio-Dirigida , Asparaginase/genética , Asparaginase/química , Asparaginase/farmacologia , Asparaginase/metabolismo , Humanos , Antineoplásicos/farmacologia , Antineoplásicos/química , Células MCF-7 , Thermococcus/enzimologia , Thermococcus/genética , Domínio Catalítico
2.
Int J Biol Macromol ; 272(Pt 1): 132654, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38810854

RESUMO

Mre11 is one of important proteins that are involved in DNA repair and recombination by processing DNA ends to produce 3'-single stranded DNA, thus providing a platform for other DNA repair and recombination proteins. In this work, we characterized the Mre11 protein from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tba-Mre11) biochemically and dissected the roles of its four conserved residues, which is the first report on Mre11 proteins from Thermococcus. Tba-Mre11 possesses exonuclease activity for degrading ssDNA and dsDNA in the 5'-3' direction, which contrasts with other reported Mre11 homologs. Maximum degradation efficiency was observed with Mn2+ at 80 °C and at pH 7.5-9.5. In addition to possessing 5'-3' exonuclease activity, Tba-Mre11 has endonuclease activity that nicks plasmid DNA and circular ssDNA. Mutational data show that residues D10, D51 and N86 in Tba-Mre11 are essential for DNA degradation since almost no activity was observed for the D10A, D51A and N86A mutants. By comparison, residue D44 in Tba-Mre11 is not responsible for DNA degradation since the D44A mutant possessed the similar WT protein activity. Notably, the D44A mutant almost completely abolished the ability to bind DNA, suggesting that residue D44 is essential for binding DNA.


Assuntos
Proteínas Arqueais , DNA de Cadeia Simples , Thermococcus , Thermococcus/enzimologia , Thermococcus/genética , Proteínas Arqueais/metabolismo , Proteínas Arqueais/química , Proteínas Arqueais/genética , DNA de Cadeia Simples/metabolismo , Exodesoxirribonucleases/metabolismo , Exodesoxirribonucleases/genética , Exodesoxirribonucleases/química , Sequência de Aminoácidos , Endonucleases/metabolismo , Endonucleases/química , Endonucleases/genética , Mutação , Endodesoxirribonucleases
3.
Int J Mol Sci ; 25(8)2024 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-38673759

RESUMO

This study investigated the effect of polycationic and uncharged polymers (and oligomers) on the catalytic parameters and thermostability of L-asparaginase from Thermococcus sibiricus (TsA). This enzyme has potential applications in the food industry to decrease the formation of carcinogenic acrylamide during the processing of carbohydrate-containing products. Conjugation with the polyamines polyethylenimine and spermine (PEI and Spm) or polyethylene glycol (PEG) did not significantly affect the secondary structure of the enzyme. PEG contributes to the stabilization of the dimeric form of TsA, as shown by HPLC. Furthermore, neither polyamines nor PEG significantly affected the binding of the L-Asn substrate to TsA. The conjugates showed greater maximum activity at pH 7.5 and 85 °C, 10-50% more than for native TsA. The pH optima for both TsA-PEI and TsA-Spm conjugates were shifted to lower pH ranges from pH 10 (for the native enzyme) to pH 8.0. Additionally, the TsA-Spm conjugate exhibited the highest activity at pH 6.5-9.0 among all the samples. Furthermore, the temperature optimum for activity at pH 7.5 shifted from 90-95 °C to 80-85 °C for the conjugates. The thermal inactivation mechanism of TsA-PEG appeared to change, and no aggregation was observed in contrast to that of the native enzyme. This was visually confirmed and supported by the analysis of the CD spectra, which remained almost unchanged after heating the conjugate solution. These results suggest that TsA-PEG may be a more stable form of TsA, making it a potentially more suitable option for industrial use.


Assuntos
Asparaginase , Biocatálise , Estabilidade Enzimática , Thermococcus , Asparaginase/química , Asparaginase/metabolismo , Thermococcus/enzimologia , Concentração de Íons de Hidrogênio , Polietilenoglicóis/química , Temperatura , Proteínas Arqueais/química , Proteínas Arqueais/metabolismo
4.
Proteins ; 92(7): 808-818, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38333996

RESUMO

Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic "isoprenol pathways," which seek to reduce the synthesis of the isoprenoid precursors to two enzymatic steps. Furthermore, the natural promiscuity of IPKs toward non-natural alkyl-monophosphates (alkyl-Ps) as substrates has hinted at the isoprenol pathways' potential to access novel isoprenoids with potentially useful activities. However, only a handful of IPK crystal structures have been solved to date, and even fewer of these contain non-natural substrates bound in the active site. The current study sought to elucidate additional ternary complexes bound to non-natural substrates using the IPK homolog from Thermococcus paralvinellae (TcpIPK). Four such structures were solved, each bound to a different non-natural alkyl-P and the phosphoryl donor substrate/product adenosine triphosphate (ATP)/adenosine diphosphate (ADP). As expected, the quaternary, tertiary, and secondary structures of TcpIPK closely resembled those of IPKs published previously, and kinetic analysis of a novel alkyl-P substrate highlighted the potentially dramatic effects of altering the core scaffold of the natural substrate. Even more interesting, though, was the discovery of a trend correlating the position of two α helices in the active site with the magnitude of an IPK homolog's reaction rate for the natural reaction. Overall, the current structures of TcpIPK highlight the importance of continued structural analysis of the IPKs to better understand and optimize their activity with both natural and non-natural substrates.


Assuntos
Trifosfato de Adenosina , Domínio Catalítico , Thermococcus , Especificidade por Substrato , Thermococcus/enzimologia , Trifosfato de Adenosina/metabolismo , Trifosfato de Adenosina/química , Cristalografia por Raios X , Modelos Moleculares , Ligação Proteica , Cinética , Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Proteínas Arqueais/genética , Hemiterpenos/metabolismo , Hemiterpenos/química , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/genética , Conformação Proteica em alfa-Hélice , Difosfato de Adenosina/metabolismo , Difosfato de Adenosina/química , Clonagem Molecular , Expressão Gênica , Conformação Proteica em Folha beta , Sequência de Aminoácidos , Escherichia coli/genética , Escherichia coli/metabolismo , Escherichia coli/enzimologia , Proteínas Quinases
5.
Res Microbiol ; 175(5-6): 104189, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38403006

RESUMO

Archaeal NurA protein plays a key role in producing 3'-single stranded DNA used for homologous recombination repair, together with HerA, Mre11, and Rad50. Herein, we describe biochemical characteristics and roles of key amino acid residues of the NurA protein from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tba-NurA). Tba-NurA possesses 5'-3' exonuclease activity for degrading DNA, displaying maximum efficiency at 45 °C-65 °C and at pH 8.0 in the presence of Mn2+. The thermostable Tba-NurA also possesses endonuclease activity capable of nicking plasmid DNA and circular ssDNA. Mutational data demonstrate that residue D49 of Tba-NurA is essential for exonuclease activity and is involved in binding ssDNA since the D49A mutant lacked exonuclease activity and reduced ssDNA binding. The R96A and R129A mutants had no detectable dsDNA binding, suggesting that residues R96 and R129 are important for binding dsDNA. The abolished degradation activity and reduced dsDNA binding of the D120A mutant suggest that residue D120 is essential for degradation activity and dsDNA binding. Additionally, residues Y392 and H400 are important for exonuclease activity since these mutations resulted in exonuclease activity loss. To our knowledge, it is the first report on biochemical characterization and mutational analysis of the NurA protein from Thermococcus.


Assuntos
Proteínas Arqueais , DNA de Cadeia Simples , Thermococcus , Thermococcus/genética , Thermococcus/metabolismo , Thermococcus/enzimologia , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Proteínas Arqueais/química , DNA de Cadeia Simples/metabolismo , DNA de Cadeia Simples/genética , Análise Mutacional de DNA , Concentração de Íons de Hidrogênio , Exonucleases/metabolismo , Exonucleases/genética , Exonucleases/química , Temperatura , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Proteínas de Ligação a DNA/química , Ligação Proteica , DNA Arqueal/genética , DNA Arqueal/química , Endonucleases/genética , Endonucleases/metabolismo , Endonucleases/química
6.
Proteins ; 92(6): 768-775, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38235908

RESUMO

The biosynthesis pathways of coenzyme A (CoA) in most archaea involve several unique enzymes including dephospho-CoA kinase (DPCK) that converts dephospho-CoA to CoA in the final step of CoA biosynthesis in all domains of life. The archaeal DPCK is unrelated to the analogous bacterial and eukaryotic enzymes and shows no significant sequence similarity to any proteins with known structures. Unusually, the archaeal DPCK utilizes GTP as the phosphate donor although the analogous bacterial and eukaryotic enzymes are ATP-dependent kinases. Here, we report the crystal structure of DPCK and its complex with GTP and a magnesium ion from the archaeal hyperthermophile Thermococcus kodakarensis. The crystal structure demonstrates why GTP is the preferred substrate of this kinase. We also report the activity analyses of site-directed mutants of crucial residues determined based on sequence conservation and the crystal structure. From these results, the key residues involved in the reaction of phosphoryl transfer and the possible dephospho-CoA binding site are inferred.


Assuntos
Sequência de Aminoácidos , Proteínas Arqueais , Guanosina Trifosfato , Magnésio , Modelos Moleculares , Fosfotransferases (Aceptor do Grupo Álcool) , Thermococcus , Thermococcus/enzimologia , Thermococcus/genética , Thermococcus/química , Cristalografia por Raios X , Guanosina Trifosfato/metabolismo , Guanosina Trifosfato/química , Fosfotransferases (Aceptor do Grupo Álcool)/química , Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo , Fosfotransferases (Aceptor do Grupo Álcool)/genética , Proteínas Arqueais/química , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Magnésio/metabolismo , Magnésio/química , Mutagênese Sítio-Dirigida , Domínio Catalítico , Sítios de Ligação , Especificidade por Substrato , Coenzima A/metabolismo , Coenzima A/química , Ligação Proteica
7.
J Biol Chem ; 300(1): 105503, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38013090

RESUMO

Hyperthermophilic organisms thrive in extreme environments prone to high levels of DNA damage. Growth at high temperature stimulates DNA base hydrolysis resulting in apurinic/apyrimidinic (AP) sites that destabilize the genome. Organisms across all domains have evolved enzymes to recognize and repair AP sites to maintain genome stability. The hyperthermophilic archaeon Thermococcus kodakarensis encodes several enzymes to repair AP site damage including the essential AP endonuclease TK endonuclease IV. Recently, using functional genomic screening, we discovered a new family of AP lyases typified by TK0353. Here, using biochemistry, structural analysis, and genetic deletion, we have characterized the TK0353 structure and function. TK0353 lacks glycosylase activity on a variety of damaged bases and is therefore either a monofunctional AP lyase or may be a glycosylase-lyase on a yet unidentified substrate. The crystal structure of TK0353 revealed a novel fold, which does not resemble other known DNA repair enzymes. The TK0353 gene is not essential for T. kodakarensis viability presumably because of redundant base excision repair enzymes involved in AP site processing. In summary, TK0353 is a novel AP lyase unique to hyperthermophiles that provides redundant repair activity necessary for genome maintenance.


Assuntos
DNA Liase (Sítios Apurínicos ou Apirimidínicos) , Thermococcus , Desoxirribonuclease IV (Fago T4-Induzido) , Dano ao DNA , Reparo do DNA , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/química , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/genética , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/metabolismo , Thermococcus/enzimologia , Thermococcus/genética
8.
Int J Mol Sci ; 24(11)2023 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-37298582

RESUMO

L-asparaginases (L-ASNases) of microbial origin are the mainstay of blood cancer treatment. Numerous attempts have been performed for genetic improvement of the main properties of these enzymes. The substrate-binding Ser residue is highly conserved in L-ASNases regardless of their origin or type. However, the residues adjacent to the substrate-binding Ser differ between mesophilic and thermophilic L-ASNases. Based on our suggestion that the triad, including substrate-binding Ser, either GSQ for meso-ASNase or DST for thermo-ASNase, is tuned for efficient substrate binding, we constructed a double mutant of thermophilic L-ASNase from Thermococcus sibiricus (TsA) with a mesophilic-like GSQ combination. In this study, the conjoint substitution of two residues adjacent to the substrate-binding Ser55 resulted in a significant increase in the activity of the double mutant, reaching 240% of the wild-type enzyme activity at the optimum temperature of 90 °C. The mesophilic-like GSQ combination in the rigid structure of the thermophilic L-ASNase appears to be more efficient in balancing substrate binding and conformational flexibility of the enzyme. Along with increased activity, the TsA D54G/T56Q double mutant exhibited enhanced cytotoxic activity against cancer cell lines with IC90 values from 2.8- to 7.4-fold lower than that of the wild-type enzyme.


Assuntos
Asparaginase , Proteínas de Bactérias , Thermococcus , Thermococcus/enzimologia , Asparaginase/química , Asparaginase/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Ligação Proteica , Mutação , Estabilidade Enzimática/genética , Sítios de Ligação , Conformação Proteica , Especificidade por Substrato/genética
9.
Proc Natl Acad Sci U S A ; 119(32): e2207581119, 2022 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-35917344

RESUMO

Transcription must be properly regulated to ensure dynamic gene expression underlying growth, development, and response to environmental cues. Regulation is imposed throughout the transcription cycle, and while many efforts have detailed the regulation of transcription initiation and early elongation, the termination phase of transcription also plays critical roles in regulating gene expression. Transcription termination can be driven by only a few proteins in each domain of life. Detailing the mechanism(s) employed provides insight into the vulnerabilities of transcription elongation complexes (TECs) that permit regulated termination to control expression of many genes and operons. Here, we describe the biochemical activities and crystal structure of the superfamily 2 helicase Eta, one of two known factors capable of disrupting archaeal transcription elongation complexes. Eta retains a twin-translocase core domain common to all superfamily 2 helicases and a well-conserved C terminus wherein individual amino acid substitutions can critically abrogate termination activities. Eta variants that perturb ATPase, helicase, single-stranded DNA and double-stranded DNA translocase and termination activities identify key regions of the C terminus of Eta that, when combined with modeling Eta-TEC interactions, provide a structural model of Eta-mediated termination guided in part by structures of Mfd and the bacterial TEC. The susceptibility of TECs to disruption by termination factors that target the upstream surface of RNA polymerase and potentially drive termination through forward translocation and allosteric mechanisms that favor opening of the clamp to release the encapsulated nucleic acids emerges as a common feature of transcription termination mechanisms.


Assuntos
Proteínas Arqueais , DNA Helicases , Thermococcus , Fatores de Transcrição , Terminação da Transcrição Genética , Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Cristalografia , DNA Helicases/química , DNA Helicases/metabolismo , RNA Polimerases Dirigidas por DNA/metabolismo , Domínios Proteicos , Thermococcus/enzimologia , Thermococcus/genética , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo
10.
Int J Biochem Cell Biol ; 143: 106154, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34990837

RESUMO

Flap endonuclease 1 (FEN1) plays important roles in DNA replication, repair and recombination. Herein, we report biochemical characteristics and catalytic mechanism of a novel FEN1 from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tb-FEN1). As expected, the recombinant Tb-FEN1 can cleave 5'-flap DNA. However, the enzyme has no activity on cleaving pseudo Y DNA, which sharply contrasts with other archaeal and eukaryotic FEN1 homologs. Tb-FEN1 retains 24% relative activity after heating at 100 °C for 20 min, demonstrating that it is the most thermostable among all reported FEN1 proteins. The enzyme displays maximal activity in a wide range of pH from 7.0 to 9.5. The Tb-FEN1 activity is dependent on a divalent metal ion, among which Mg2+ and Mn2+ are optimal. Enzyme activity is inhibited by NaCl. Kinetic analyzes estimated that an activation energy for removal of 5'-flap from DNA by Tb-FEN1 was 35.7 ± 4.3 kcal/mol, which is the first report on energy barrier for excising 5'-flap from DNA by a FEN1 enzyme. Mutational studies demonstrate that the K87A, R94A and E154A amino acid substitutions abolish cleavage activity and reduce 5'-flap DNA binding efficiencies, suggesting that residues K87, R94, and E154 in Tb-FEN1 are essential for catalysis and DNA binding as well. Overall, Tb-FEN1 is an extremely thermostable endonuclease with unusual features.


Assuntos
Endonucleases Flap/metabolismo , Thermococcus/enzimologia , Humanos , Mutação , Thermococcus/patogenicidade
11.
Nucleic Acids Res ; 50(7): 3601-3615, 2022 04 22.
Artigo em Inglês | MEDLINE | ID: mdl-34568951

RESUMO

Genomic DNA replication requires replisome assembly. We show here the molecular mechanism by which CMG (GAN-MCM-GINS)-like helicase cooperates with the family D DNA polymerase (PolD) in Thermococcus kodakarensis. The archaeal GINS contains two Gins51 subunits, the C-terminal domain of which (Gins51C) interacts with GAN. We discovered that Gins51C also interacts with the N-terminal domain of PolD's DP1 subunit (DP1N) to connect two PolDs in GINS. The two replicases in the replisome should be responsible for leading- and lagging-strand synthesis, respectively. Crystal structure analysis of the DP1N-Gins51C-GAN ternary complex was provided to understand the structural basis of the connection between the helicase and DNA polymerase. Site-directed mutagenesis analysis supported the interaction mode obtained from the crystal structure. Furthermore, the assembly of helicase and replicase identified in this study is also conserved in Eukarya. PolD enhances the parental strand unwinding via stimulation of ATPase activity of the CMG-complex. This is the first evidence of the functional connection between replicase and helicase in Archaea. These results suggest that the direct interaction of PolD with CMG-helicase is critical for synchronizing strand unwinding and nascent strand synthesis and possibly provide a functional machinery for the effective progression of the replication fork.


Assuntos
DNA Helicases , DNA Polimerase Dirigida por DNA , Thermococcus , DNA Helicases/genética , DNA Helicases/metabolismo , Replicação do DNA , DNA Polimerase Dirigida por DNA/genética , Eucariotos/metabolismo , Thermococcus/enzimologia , Thermococcus/metabolismo
12.
J Am Chem Soc ; 143(42): 17761-17768, 2021 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-34637287

RESUMO

Expanding the chemical space of evolvable non-natural genetic polymers (XNAs) to include functional groups that enhance protein target binding affinity offers a promising route to therapeutic aptamers with high biological stability. Here we describe the chemical synthesis and polymerase recognition of 10 chemically diverse functional groups introduced at the C-5 position of α-l-threofuranosyl uridine nucleoside triphosphate (tUTP). We show that the set of tUTP substrates is universally recognized by the laboratory-evolved polymerase Kod-RSGA. Insights into the mechanism of TNA synthesis were obtained from a high-resolution X-ray crystal structure of the postcatalytic complex bound to the primer-template duplex. A structural analysis reveals a large cavity in the enzyme active site that can accommodate the side chain of C-5-modified tUTP substrates. Our findings expand the chemical space of evolvable nucleic acid systems by providing a synthetic route to artificial genetic polymers that are uniformly modified with diversity-enhancing functional groups.


Assuntos
DNA Polimerase Dirigida por DNA , Tetroses , Uridina Trifosfato , Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Cristalografia por Raios X , DNA Polimerase Dirigida por DNA/química , DNA Polimerase Dirigida por DNA/metabolismo , Nucleosídeos/química , Ligação Proteica , Tetroses/síntese química , Tetroses/química , Tetroses/metabolismo , Thermococcus/enzimologia , Uridina Trifosfato/análogos & derivados , Uridina Trifosfato/síntese química , Uridina Trifosfato/metabolismo
13.
Int J Mol Sci ; 22(18)2021 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-34576056

RESUMO

L-asparaginase (L-ASNase) is a vital enzyme with a broad range of applications in medicine and food industry. Drawbacks of current commercial L-ASNases stimulate the search for better-producing sources of the enzyme, and extremophiles are especially attractive in this view. In this study, a novel L-asparaginase originating from the hyperthermophilic archaeon Thermococcus sibiricus (TsA) was expressed in Escherichia coli, purified and characterized. The enzyme is optimally active at 90 °C and pH 9.0 with a specific activity of 2164 U/mg towards L-asparagine. Kinetic parameters KM and Vmax for the enzyme are 2.8 mM and 1200 µM/min, respectively. TsA is stable in urea solutions 0-6 M and displays no significant changes of the activity in the presence of metal ions Ni2+, Cu2+, Mg2+, Zn2+ and Ca2+ and EDTA added in concentrations 1 and 10 mmol/L except for Fe3+. The enzyme retains 86% of its initial activity after 20 min incubation at 90 °C, which should be enough to reduce acrylamide formation in foods processed at elevated temperatures. TsA displays strong cytotoxic activity toward cancer cell lines K562, A549 and Sk-Br-3, while normal human fibroblasts WI-38 are almost unsensitive to it. The enzyme seems to be a promising candidate for further investigation and biotechnology application.


Assuntos
Archaea/enzimologia , Asparaginase/isolamento & purificação , Biotecnologia/tendências , Thermococcus/enzimologia , Sequência de Aminoácidos/genética , Antineoplásicos/química , Antineoplásicos/farmacologia , Asparaginase/química , Asparaginase/genética , Asparagina/metabolismo , Estabilidade Enzimática/genética , Escherichia coli/efeitos dos fármacos , Cinética , Especificidade por Substrato/genética
14.
Chembiochem ; 22(21): 3060-3066, 2021 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-34486208

RESUMO

With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5'-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases.


Assuntos
DNA Arqueal/metabolismo , DNA Polimerase Dirigida por DNA/metabolismo , Replicação do DNA , DNA Arqueal/análise , DNA Polimerase Dirigida por DNA/química , Desaminação , Modelos Moleculares , Conformação de Ácido Nucleico , Thermococcus/enzimologia
15.
Sci Rep ; 11(1): 16880, 2021 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-34413335

RESUMO

Catalytically active inclusion bodies (CatIBs) produced in Escherichia coli are an interesting but currently underexplored strategy for enzyme immobilization. They can be purified easily and used directly as stable and reusable heterogenous catalysts. However, very few examples of CatIBs that are naturally formed during heterologous expression have been reported so far. Previous studies have revealed that the adenosine 5'-monophosphate phosphorylase of Thermococcus kodakarensis (TkAMPpase) forms large soluble multimers with high thermal stability. Herein, we show that heat treatment of soluble protein from crude extract induces aggregation of active protein which phosphorolyse all natural 5'-mononucleotides. Additionally, inclusion bodies formed during the expression in E. coli were found to be similarly active with 2-6 folds higher specific activity compared to these heat-induced aggregates. Interestingly, differences in the substrate preference were observed. These results show that the recombinant thermostable TkAMPpase is one of rare examples of naturally formed CatIBs.


Assuntos
Monofosfato de Adenosina/metabolismo , Biocatálise , Fosforilases/metabolismo , Thermococcus/enzimologia , Monofosfato de Adenosina/química , Monofosfato de Citidina , Estabilidade Enzimática , Corpos de Inclusão/metabolismo , Agregados Proteicos , Solubilidade , Especificidade por Substrato , Temperatura
16.
Commun Biol ; 4(1): 687, 2021 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-34099860

RESUMO

Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.


Assuntos
Aconitato Hidratase/química , Agrobacterium tumefaciens/enzimologia , Thermococcus/enzimologia , Agrobacterium tumefaciens/química , Domínio Catalítico , Cristalografia por Raios X , Evolução Molecular , Modelos Moleculares , Conformação Proteica , Thermococcus/química
17.
Angew Chem Int Ed Engl ; 60(32): 17680-17685, 2021 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-34056805

RESUMO

ß-Branched noncanonical amino acids are valuable molecules in modern drug development efforts. However, they are still challenging to prepare due to the need to set multiple stereocenters in a stereoselective fashion, and contemporary methods for the synthesis of such compounds often rely on the use of rare-transition-metal catalysts with designer ligands. Herein, we report a highly diastereo- and enantioselective biocatalytic transamination method to prepare a broad range of aromatic ß-branched α-amino acids. Mechanistic studies show that the transformation proceeds through dynamic kinetic resolution that is unique to the optimal enzyme. To highlight its utility and practicality, the biocatalytic reaction was applied to the synthesis of several sp3 -rich cyclic fragments and the first total synthesis of jomthonic acid A.


Assuntos
Aminoácidos Aromáticos/síntese química , Aminoácidos de Cadeia Ramificada/síntese química , Aminação , Aminoácidos/síntese química , Proteínas Arqueais/química , Proteínas de Bactérias/química , Biocatálise , Pyrococcus horikoshii/enzimologia , Estereoisomerismo , Thermococcus/enzimologia , Thermus thermophilus/enzimologia , Transaminases/química
18.
Biosci Biotechnol Biochem ; 85(7): 1650-1657, 2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-33942867

RESUMO

The amino acid sequence of the OCC_10945 gene product from the hyperthermophilic archaeon Thermococcus litoralis DSM5473, originally annotated as γ-aminobutyrate aminotransferase, is highly similar to that of the uncharacterized pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase from Pyrococcus horikoshii. The OCC_10945 enzyme was successfully overexpressed in Escherichia coli by coexpression with a chaperone protein. The purified enzyme demonstrated PLP-dependent amino acid racemase activity primarily toward Met and Leu. Although PLP contributed to enzyme stability, it only loosely bound to this enzyme. Enzyme activity was strongly inhibited by several metal ions, including Co2+ and Zn2+, and nonsubstrate amino acids such as l-Arg and l-Lys. These results suggest that the underlying PLP-binding and substrate recognition mechanisms in this enzyme are significantly different from those of the other archaeal and bacterial amino acid racemases. This is the first description of a novel PLP-dependent amino acid racemase with moderate substrate specificity in hyperthermophilic archaea.


Assuntos
Isomerases de Aminoácido/metabolismo , Proteínas Arqueais/metabolismo , Thermococcus/enzimologia , Isomerases de Aminoácido/química , Sequência de Aminoácidos , Proteínas Arqueais/química , Eletroforese em Gel de Poliacrilamida , Genes Arqueais , Chaperonas Moleculares/metabolismo , Filogenia , Especificidade por Substrato , Thermococcus/genética
19.
Int J Biol Macromol ; 173: 168-179, 2021 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-33444657

RESUMO

The genome sequence of Thermococcus kodakarensis contains an open reading frame, TK1110, annotated as ADP-dependent glucokinase. The encoding gene was expressed in Escherichia coli and the gene product, TK-GLK, was produced in soluble and active form. The recombinant enzyme was extremely thermostable. Thermostability was increased significantly in the presence of ammonium sulfate. ADP was the preferred co-factor for TK-GLK, which could be replaced with CDP but with a 60% activity. TK-GLK was a metal ion-dependent enzyme which exhibited glucokinase, glucosamine kinase and glucose 6-phosphatase activities. It catalyzed the phosphorylation of both glucose and glucosamine with nearly the same rate and affinity. The apparent Km values for glucose and glucosamine were 0.48 ± 0.03 and 0.47 ± 0.09 mM, respectively. The catalytic efficiency (kcat/Km) values against these two substrates were 6.2 × 105 ± 0.25 and 5.8 × 105 ± 0.75 M-1 s-1. The apparent Km value for dephosphorylation of glucose 6-phosphate was ~14-fold higher than that of glucose phosphorylation. Similarly, catalytic efficiency (kcat/Km) for phosphatase reaction was ~19-fold lower than that for the kinase reaction. To the best of our knowledge, this is the first report that describes the reversible nature of a euryarchaeal ADP-dependent glucokinase.


Assuntos
Adenosina Difosfato Glucose/química , Difosfato de Adenosina/química , Proteínas Arqueais/química , Glucoquinase/química , Glucosamina/química , Glucose/química , Thermococcus/enzimologia , Difosfato de Adenosina/metabolismo , Adenosina Difosfato Glucose/metabolismo , Sequência de Aminoácidos , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Sítios de Ligação , Biocatálise , Clonagem Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Glucoquinase/genética , Glucoquinase/metabolismo , Glucosamina/metabolismo , Glucose/metabolismo , Cinética , Simulação de Acoplamento Molecular , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Thermococcus/química , Termodinâmica
20.
Int J Biol Macromol ; 171: 491-501, 2021 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-33428959

RESUMO

The genome of the hyperthermophilic and piezophilic euryarchaeaon Thermococcus barophilus Ch5 encodes three putative alcohol dehydrogenases (Tba ADHs). Herein, we characterized Tba ADH547 biochemically and probed its catalytic mechanism by mutational studies. Our data demonstrate that Tba ADH547 can oxidize ethanol and reduce acetaldehyde at high temperature with the same optimal temperature (75 °C) and exhibit similar thermostability for oxidization and reduction reactions. However, Tba ADH547 has different optimal pH for oxidation and reduction: 8.5 for oxidation and 7.0 for reduction. Tba ADH547 is dependent on a divalent ion for its oxidation activity, among which Mn2+ is optimal. However, Tba ADH547 displays about 20% reduction activity without a divalent ion, and the maximal activity with Fe2+. Furthermore, Tba ADH547 showcases a strong substrate preference for 1-butanol and 1-hexanol over ethanol and other alcohols. Similarly, Tba ADH547 prefers butylaldehyde to acetaldehyde as its reduction substrate. Mutational studies showed that the mutations of residues D195, H199, H262 and H274 to Ala result in the significant activity loss of Tba ADH547, suggesting that residues D195, H199, H262 and H274 are responsible for catalysis. Overall, Tba ADH547 is a thermoactive ADH with novel biochemical characteristics, thereby allowing this enzyme to be a potential biocatalyst.


Assuntos
Aldeído Oxirredutases/isolamento & purificação , Proteínas Arqueais/isolamento & purificação , Thermococcus/enzimologia , Álcoois/metabolismo , Aldeído Oxirredutases/genética , Aldeído Oxirredutases/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Sequência de Bases , Cátions/farmacologia , Dicroísmo Circular , Sequência Conservada , Genes Arqueais , Temperatura Alta , Concentração de Íons de Hidrogênio , Cinética , Mutagênese Sítio-Dirigida , Filogenia , Desnaturação Proteica , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Thermococcales/enzimologia , Thermococcales/genética , Thermococcus/genética
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