Single‐strand‐specific DNase activity is an inherent property of the 140‐kDa protein of the snake venom exonuclease<sup>1</sup>

Stoynov, Stoyno; Bakalova, A.; Dimov, S.; Mitkova, A.; Dolapchiev, Luben B.

doi:10.1016/s0014-5793(97)00489-4

Cited by 17 publications

(7 citation statements)

References 9 publications

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“…The nuclease-like domain retains neither the catalytic histidine nor its tyrosine counterpart and is presumed to be catalytically inactive. Interestingly, this cluster also includes proteins that function as venom phosphodiesterases in snakes and a variety of marine species (accession: J3SBP3) ( 87 ).…”

Section: Resultsmentioning

confidence: 99%

Systematic classification of the His-Me finger superfamily

Jabłońska

Matelska

Steczkiewicz

et al. 2017

Nucleic Acids Research

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The His-Me finger endonucleases, also known as HNH or ββα-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron homing, host defense and target offense. Its overall structural compactness and non-specificity make it a perfectly-tailored pathogenic module that participates on both sides of inter- and intra-organismal competition. An extremely low sequence similarity across the superfamily makes it difficult to identify and classify new His-Me fingers. Using state-of-the-art distant homology detection methods, we provide an updated and systematic classification of His-Me finger proteins. In this work, we identified over 100 000 proteins and clustered them into 38 groups, of which three groups are new and cannot be found in any existing public domain database of protein families. Based on an analysis of sequences, structures, domain architectures, and genomic contexts, we provide a careful functional annotation of the poorly characterized members of this superfamily. Our results may inspire further experimental investigations that should address the predicted activity and clarify the potential substrates, to provide more detailed insights into the fundamental biological roles of these proteins.

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Section: Resultsmentioning

confidence: 99%

Systematic classification of the His-Me finger superfamily

Jabłońska

Matelska

Steczkiewicz

et al. 2017

Nucleic Acids Research

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“…Stereo configuration of the phosphorothioate group can be determined due to more efficient digestion of the R p compared to the S p configuration [ 38 ]. Snake venom phosphodiesterase from Crotalus adamanteus can also act as an endonuclease on single-stranded oligonucleotides [ 39 , 40 ]. Digestions were performed at high enzyme concentration and long reaction times in order to completely digest unmodified oligonucleotides as well as modified oligonucleotides in R p configuration.…”

Section: Determination Of Stereo Configuration Using Enzymatic Assaymentioning

confidence: 99%

Investigation of factors influencing the separation of diastereomers of phosphorothioated oligonucleotides

et al. 2019

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This study presents a systematic investigation of factors influencing the chromatographic separation of diastereomers of phosphorothioated pentameric oligonucleotides as model solutes. Separation was carried out under ion-pairing conditions using an XBridge C 18 column. For oligonucleotides with a single sulfur substitution, the diastereomer selectivity was found to increase with decreasing carbon chain length of the tertiary alkylamine used as an ion-pair reagent. Using an ion-pair reagent with high selectivity for diastereomers, triethylammonium, it was found the selectivity increased with decreased ion-pair concentration and shallower gradient slope. Selectivity was also demonstrated to be dependent on the position of the modified linkage. Substitutions at the center of the pentamer resulted in higher diastereomer selectivity compared to substitutions at either end. For mono-substituted oligonucleotides, the retention order and stereo configuration were consistently found to be correlated, with R p followed by S p, regardless of which linkage was modified. The type of nucleobase greatly affects the observed selectivity. A pentamer of cytosine has about twice the diastereomer selectivity of that of thymine. When investigating the retention of various oligonucleotides eluted using tributylammonium as the ion-pairing reagent, no diastereomer selectivity could be observed. However, retention was found to be dependent on both the degree and position of sulfur substitution as well as on the nucleobase. When analyzing fractions collected in the front and tail of overloaded injections, a significant difference was found in the ratio between R p and S p diastereomers, indicating that the peak broadening observed when using tributylammonium could be explained by partial diastereomer separation. Electronic supplementary material The online version of this article (10.1007/s00216-019-01813-2) contains supplementary material, which is available to authorized users.

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“…Extracellular PDEs known as exonucleases, exist in venoms and their route in envenomation is mostly by attacking nucleic acids [6]through removal of mononucleotide units from the polynucleotide chain in a stepwise fashion [7, 8]. They also possess the endonucleolytic activity towards single‐stranded DNA [9]and as such they have been used for sequencing oligonucleotides and polynucleotides [10–13]. Many selective inhibitors of each isoenzyme of intracellular PDEs have been developed, which have many advantages in clinical use [14–16].…”

Section: Introductionmentioning

confidence: 99%

Enhancement and inhibition of snake venom phosphodiesterase activity by lysophospholipids

Mamillapalli¹,

Haimovitz²,

Mazor³

et al. 1998

FEBS Letters

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Lysophospholipids are liberated during venomous action. In this study we demonstrated that lysophosphatidyl choline (LPC) of various acyl chains enhances considerably the activity of snake venom phosphodiesterase (PDE). Lysophosphatidic acid (LPA) and its cyclic form (cLPA), on the other hand, were found to inhibit this enzyme in a non-competitive (LPA) or competitive (cLPA) manner. Both of these activities may contribute to the progression and subsidence of the poisoning profile. PDE from cellular origin was not substantially affected by any of the above lysophospholipids.z 1998 Federation of European Biochemical Societies.

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Single‐strand‐specific DNase activity is an inherent property of the 140‐kDa protein of the snake venom exonuclease¹

Cited by 17 publications

References 9 publications

Systematic classification of the His-Me finger superfamily

Systematic classification of the His-Me finger superfamily

Investigation of factors influencing the separation of diastereomers of phosphorothioated oligonucleotides

Enhancement and inhibition of snake venom phosphodiesterase activity by lysophospholipids

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Single‐strand‐specific DNase activity is an inherent property of the 140‐kDa protein of the snake venom exonuclease1

Cited by 17 publications

References 9 publications

Systematic classification of the His-Me finger superfamily

Systematic classification of the His-Me finger superfamily

Investigation of factors influencing the separation of diastereomers of phosphorothioated oligonucleotides

Enhancement and inhibition of snake venom phosphodiesterase activity by lysophospholipids

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Single‐strand‐specific DNase activity is an inherent property of the 140‐kDa protein of the snake venom exonuclease¹