Crystallization and preliminary X-ray diffraction analysis of a novel sphingomyelinase D from<i>Loxosceles gaucho</i>venom

Ullah, Anwar; Magalhães, Geraldo Santana; Masood, Rehana; Mariutti, Ricardo Barros; Coronado, Mônika A.; Murakami, Mário Tyago; Barbaro, Kátia Cristina; Arni, Raghuvir K.

doi:10.1107/s2053230x14019207

Cited by 8 publications

(4 citation statements)

References 18 publications

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“…Snake venom is a crude mixture that contains enzymatic and non-enzymatic proteins, peptides, organic compounds of low molecular weight, and inorganic compounds [1,2]. Proteins constitute the major portion (about 90%) of the total dry mass of crude snake venom, with or without catalytic activity, including neurotoxins, cardiotoxins, C-type lectins, proteinases, metalloproteinases, serine proteinases, phospholipases, hyaluronidases, acetylcholinesterases, L-amino acid oxidases, three-finger toxins, phospholipase A 2 s, and nucleases [3,4,5,6,7,8,9]. Metalloproteinases, serine proteinases, phospholipases, and neurotoxins are the most widely studied snake venom proteins, as they occur in high concentrations and are relatively easy to purify [1,2,3,4,5,10,11,12].…”

Section: Introductionmentioning

confidence: 99%

The Sequence and a Three-Dimensional Structural Analysis Reveal Substrate Specificity among Snake Venom Phosphodiesterases

Ullah

Ali

et al. 2019

Toxins

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(1) Background. Snake venom phosphodiesterases (SVPDEs) are among the least studied venom enzymes. In envenomation, they display various pathological effects, including induction of hypotension, inhibition of platelet aggregation, edema, and paralysis. Until now, there have been no 3D structural studies of these enzymes, thereby preventing structure–function analysis. To enable such investigations, the present work describes the model-based structural and functional characterization of a phosphodiesterase from Crotalus adamanteus venom, named PDE_Ca. (2) Methods. The PDE_Ca structure model was produced and validated using various software (model building: I-TESSER, MODELLER 9v19, Swiss-Model, and validation tools: PROCHECK, ERRAT, Molecular Dynamic Simulation, and Verif3D). (3) Results. The proposed model of the enzyme indicates that the 3D structure of PDE_Ca comprises four domains, a somatomedin B domain, a somatomedin B-like domain, an ectonucleotide pyrophosphatase domain, and a DNA/RNA non-specific domain. Sequence and structural analyses suggest that differences in length and composition among homologous snake venom sequences may account for their differences in substrate specificity. Other properties that may influence substrate specificity are the average volume and depth of the active site cavity. (4) Conclusion. Sequence comparisons indicate that SVPDEs exhibit high sequence identity but comparatively low identity with mammalian and bacterial PDEs.

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Section: Introductionmentioning

confidence: 99%

The Sequence and a Three-Dimensional Structural Analysis Reveal Substrate Specificity among Snake Venom Phosphodiesterases

Ullah

Ali

et al. 2019

Toxins

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“…These PLDs contain between 284 and 285 amino acid residues, and are organized as a barrel formed by 8 parallel beta strands linked to alpha helices, resulting in a general fold referred to as (alpha/beta) 8 or a Triose Phosphate Isomerase (TIM) barrel. PLDs share structural homology with TIM, an enzyme with a similar three-dimensional fold [5,[62][63][64][65]. The amino acid residues involved in the catalytic activity of these PLDs (His12, Glu32, Asp34, Asp91, His47, Asp52, Trp230, Asp233, and Asn252) [62] are well conserved in all isoforms of Loxosceles PLDs identified to date [5,61].…”

Section: Structural Organization and The Catalytic Mechanisms Of Browmentioning

confidence: 99%

Forty Years of the Description of Brown Spider Venom Phospholipases-D

Gremski

Justa

Silva

et al. 2020

Toxins

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Spiders of the genus Loxosceles, popularly known as Brown spiders, are considered a serious public health issue, especially in regions of hot or temperate climates, such as parts of North and South America. Although the venoms of these arachnids are complex in molecular composition, often containing proteins with distinct biochemical characteristics, the literature has primarily described a family of toxins, the Phospholipases-D (PLDs), which are highly conserved in all Loxosceles species. PLDs trigger most of the major clinical symptoms of loxoscelism i.e., dermonecrosis, thrombocytopenia, hemolysis, and acute renal failure. The key role played by PLDs in the symptomatology of loxoscelism was first described 40 years ago, when researches purified a hemolytic toxin that cleaved sphingomyelin and generated choline, and was referred to as a Sphingomyelinase-D, which was subsequently changed to Phospholipase-D when it was demonstrated that the enzyme also cleaved other cellular phospholipids. In this review, we present the information gleaned over the last 40 years about PLDs from Loxosceles venoms especially with regard to the production and characterization of recombinant isoforms. The history of obtaining these toxins is discussed, as well as their molecular organization and mechanisms of interaction with their substrates. We will address cellular biology aspects of these toxins and how they can be used in the development of drugs to address inflammatory processes and loxoscelism. Present and future aspects of loxoscelism diagnosis will be discussed, as well as their biotechnological applications and actions expected for the future in this field.

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“…Crystal structure of LiRecDT1 from L. intermedia was published by de Giuseppe et al [ 108 ], indicating that this toxin contained an additional disulfide bond in the toxin structure catalytic loop compared with the previously described phospholipase-D from L. laeta [ 109 , 110 ]. The phospholipase-D from L. gaucho was also crystallized by Ullah et al [ 111 ] in 2014 and the structure was shown to be very similar to the phospholipase-D from L. intermedia [ 112 ] .…”

Section: History Of the Brown Spider Venom Toxinologymentioning

confidence: 99%

Highlights in the knowledge of brown spider toxins

Chaves-Moreira

Senff‐Ribeiro

Wille

et al. 2017

J Venom Anim Toxins Incl Trop Dis

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Brown spiders are venomous arthropods that use their venom for predation and defense. In humans, bites of these animals provoke injuries including dermonecrosis with gravitational spread of lesions, hematological abnormalities and impaired renal function. The signs and symptoms observed following a brown spider bite are called loxoscelism. Brown spider venom is a complex mixture of toxins enriched in low molecular mass proteins (4–40 kDa). Characterization of the venom confirmed the presence of three highly expressed protein classes: phospholipases D, metalloproteases (astacins) and insecticidal peptides (knottins). Recently, toxins with low levels of expression have also been found in Loxosceles venom, such as serine proteases, protease inhibitors (serpins), hyaluronidases, allergen-like toxins and histamine-releasing factors. The toxin belonging to the phospholipase-D family (also known as the dermonecrotic toxin) is the most studied class of brown spider toxins. This class of toxins single-handedly can induce inflammatory response, dermonecrosis, hemolysis, thrombocytopenia and renal failure. The functional role of the hyaluronidase toxin as a spreading factor in loxoscelism has also been demonstrated. However, the biological characterization of other toxins remains unclear and the mechanism by which Loxosceles toxins exert their noxious effects is yet to be fully elucidated. The aim of this review is to provide an insight into brown spider venom toxins and toxicology, including a description of historical data already available in the literature. In this review article, the identification processes of novel Loxosceles toxins by molecular biology and proteomic approaches, their biological characterization and structural description based on x-ray crystallography and putative biotechnological uses are described along with the future perspectives in this field.

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Crystallization and preliminary X-ray diffraction analysis of a novel sphingomyelinase D fromLoxosceles gauchovenom

Cited by 8 publications

References 18 publications

The Sequence and a Three-Dimensional Structural Analysis Reveal Substrate Specificity among Snake Venom Phosphodiesterases

The Sequence and a Three-Dimensional Structural Analysis Reveal Substrate Specificity among Snake Venom Phosphodiesterases

Forty Years of the Description of Brown Spider Venom Phospholipases-D

Highlights in the knowledge of brown spider toxins

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