Structure of nucleoside diphosphate kinase from pacific shrimp (<i>Litopenaeus vannamei</i>) in binary complexes with purine and pyrimidine nucleoside diphosphates

López-Zavala, Alonso A.; Quintero-Reyes, Idania E.; Carrasco-Miranda, J.S.; Stojanoff, V.; Weichsel, A.; Rudino‐Pinera, E.; Sotelo‐Mundo, Rogerio R.

doi:10.1107/s2053230x1401557x

Cited by 5 publications

(2 citation statements)

References 33 publications

(50 reference statements)

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“…In the Pp AK-Arg structure we found that Glu225 is positioned in a similar way, making only one salt-bridge with NH 2 (ω)-1 of the arginine guanidino group end. This small local conformational change was also observed in Lv AK-Arg structure and it is postulated to lead to a productive active site in the closed conformation ( López-Zavala et al, 2014 ; Zhou et al, 1998 ).…”

Section: Discussionsupporting

confidence: 52%

Biochemical and structural characterization of a novel arginine kinase from the spiderPolybetes pythagoricus

Laino

López-Zavala

García-Orozco

et al. 2017

PeerJ

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Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus (PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, and it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant (Km) was 1.7 mM with a kcat of 75 s−1. Two crystal structures are presented, the apoPvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310–320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Finally, these results contribute to knowledge of mechanistic details of the function of arginine kinase.

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Section: Discussionsupporting

confidence: 52%

Biochemical and structural characterization of a novel arginine kinase from the spiderPolybetes pythagoricus

Laino

López-Zavala

García-Orozco

et al. 2017

PeerJ

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“…Noticeably, drug metabolism might be hindered due to the significantly downregulation of a kinase gene. The kinase (EC 2.7.4.6) is a nucleoside-diphosphate kinase, catalyzing phosphorylation of nucleoside diphosphates to nucleoside triphosphates for DNA replication [ 46 ]. Understanding why these genes were downregulated in oxamyl-treated TPBs cannot be ignored in further studies.…”

Section: Resultsmentioning

confidence: 99%

Microarray and Functional Pathway Analyses Revealed Significantly Elevated Gene Expressions Associated with Metabolic Resistance to Oxamyl (Vydate) in Lygus lineolaris

Zhu,

Du,

Liu

et al. 2024

Toxics

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The tarnished plant bug (TPB, Lygus lineolaris) remains a major pest for a variety of crops. Frequent sprays on row crops, especially cotton, prompted resistance development in field populations. To maintain chemical control as an effective tool against the pest, knowledge of global gene regulations is desirable for better understanding and managing the resistance. Novel microarray expressions of 6688 genes showed 685 significantly upregulated and 1382 significantly downregulated genes in oxamyl-selected TPBs (Vyd1515FF[R]) from a cotton field. Among the 685 upregulated genes (participated in 470 pathways), 176 genes code 30 different enzymes, and 7 of the 30 participate in 24 metabolic pathways. Six important detoxification pathways were controlled by 20 genes, coding 11 esterases, two P450s, two oxidases, and three pathway-associated enzymes (synthases, reductase, and dehydrogenase). Functional analyses showed substantially enhanced biological processes and molecular functions, with hydrolase activity as the most upregulated molecular function (controlled by 166 genes). Eleven esterases belong to the acting on ester bond subclass of the 166 hydrolases. Surprisingly, only one GST showed significant upregulation, but it was not involved in any detoxification pathway. Therefore, this research reports a set of 20 genes coding 6 enzyme classes to detoxify a carbamate insecticide oxamyl in Vyd1515FF. Together with three previous reports, we have obtained the best knowledge of resistance mechanisms to all four conventional insecticide classes in the economically important crop pest. This valuable finding will greatly facilitate the development of molecular tools to monitor and manage the resistance and to minimize risk to environment.

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A novel viral thymidylate kinase with dual kinase activity

Guevara-Hernández

Arvizu‐Flores

Lugo‐Sánchez

et al. 2015

J Bioenerg Biomembr

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Nucleotide phosphorylation is a key step in DNA replication and viral infections, since suitable levels of nucleotide triphosphates pool are required for this process. Deoxythymidine monophosphate (dTMP) is produced either by de novo or salvage pathways, which is further phosphorylated to deoxythymidine triphosphate (dTTP). Thymidyne monophosphate kinase (TMK) is the enzyme in the junction of both pathways, which phosphorylates dTMP to yield deoxythymidine diphosphate (dTDP) using adenosine triphosphate (ATP) as a phosphate donor. White spot syndrome virus (WSSV) genome contains an open reading frame (ORF454) that encodes a thymidine kinase and TMK domains in a single polypeptide. We overexpressed the TMK ORF454 domain (TMKwssv) and its specific activity was measured with dTMP and dTDP as phosphate acceptors. We found that TMKwssv can phosphorylate dTMP to yield dTDP and also is able to use dTDP as a substrate to produce dTTP. Kinetic parameters K M and k cat were calculated for dTMP (110 μM, 3.6 s(-1)), dTDP (251 μM, 0.9 s(-1)) and ATP (92 μM, 3.2 s(-1)) substrates, and TMKwssv showed a sequential ordered bi-bi reaction mechanism. The binding constants K d for dTMP (1.9 μM) and dTDP (10 μM) to TMKwssv were determined by Isothermal Titration Calorimetry. The affinity of the nucleotidic analog stavudine monophosphate was in the same order of magnitude (K d 3.6 μM) to the canonical substrate dTMP. These results suggest that nucleotide analogues such as stavudine could be a suitable antiviral strategy for the WSSV-associated disease.

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Structure of nucleoside diphosphate kinase from pacific shrimp (Litopenaeus vannamei) in binary complexes with purine and pyrimidine nucleoside diphosphates

Cited by 5 publications

References 33 publications

Biochemical and structural characterization of a novel arginine kinase from the spiderPolybetes pythagoricus

Biochemical and structural characterization of a novel arginine kinase from the spiderPolybetes pythagoricus

Microarray and Functional Pathway Analyses Revealed Significantly Elevated Gene Expressions Associated with Metabolic Resistance to Oxamyl (Vydate) in Lygus lineolaris

A novel viral thymidylate kinase with dual kinase activity

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