Homology Modelling of Lycopene Cleavage Oxygenase: The Key Enzyme of Bixin Production

Satpathy, Raghunath

doi:10.4172/jcsb.1000057

Cited by 5 publications

(5 citation statements)

References 17 publications

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“…At this discussion, only studies that evaluate the Build Homology Modeling protocol models have been presented here. The models construction (using Build Homology Modeling protocol) and evaluation studies which have a similarity with our PROCHECK results are from Patel et al [35], Khatri et al [36], Satpathy et al [37], and Singh et al [38]. The amylase, ninjurin, lycopene, and H1N1 nucleocapsid models have been generated in those experiments.…”

Section: Discussionmentioning

confidence: 56%

Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase

Herlambang¹,

Saleh²

2012

JBPC

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Protein structure modeling using a homologous template is one of many routines that accompany the molecular dynamics simulation for biological material. There are currently two protocols of protein modeling available in Accelrys Discovery Studio 2.1, Build Mutants and Build Homology Modeling protocols. Both are template-based modeling, but with a different process. In this study, two different templates, 3CKZ and 274Y, have been used to see how much the differences will be made by those two protocols if the templates has significant percentage of identity. Evaluation of structure models has been performed using DOPE score, 3D-profile, and PROCHECK. The results indicated that Build Mutants Protocols produces more stable structures but has a low reliability values and low quality of stereochemistry when using a template that has a lower percentage of identity. The results also yield more stable, reliable, and higher percentage of residues in most favoured and additionally allowed region for the usage of Build Homology Modeling Protocol on both templates. These observations suggest that Build Homology Modeling protocol is recommended for protein modeling

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Section: Discussionmentioning

confidence: 56%

Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase

Herlambang¹,

Saleh²

2012

JBPC

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“…4C). A number of specialized plant CCDs have also been identified, such as CCD2 from Crocus sativus, which cleaves zeaxanthin during corcin biosynthesis (Frusciante et al, 2014), and lycopene cleavage dioxygenase from Bixa orellana, which is capable of cleaving the b-carotenoid precursor (Satpathy et al, 2010).…”

Section: Carotenoid Cleavage Dioxygenasesmentioning

confidence: 99%

Unleashing the Synthetic Power of Plant Oxygenases: From Mechanism to Application

Mitchell

Weng

2019

Plant Physiol.

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ORCID IDs: 0000-0003-3726-6569 (A.J.M.); 0000-0003-3059-0075 (J.-K.W.).Plant-specialized metabolites account for arguably the largest and most diverse pool of natural products accessible to humans. Conferring the plants' selective traits, such as UV defense, pathogen resistance, and enhanced nutrient uptake, these chemicals are crucial to a species' viability. During biosynthesis of these compounds, a vast array of specialized enzymes catalyze diverse chemical modifications, with oxidation being one of the most predominant (Smanski et al., 2016;Dong et al., 2018). Considering these observations, it is not surprising that within plant genomes, two families of oxygenases are the most abundant: the cytochrome P450 monooxygenases (P450s) and the iron/2-oxoglutaratedependent oxygenases (Fe/2OGs). These and other oxygenases represent the synthetic workhorses of plantspecialized metabolism and also play key roles in primary metabolism, cellular regulation, and fitness. Furthermore, the challenging and selective chemistry they catalyze cannot currently be matched by synthetic chemists. Since many plant natural products serve as valuable pharmaceuticals and commodity chemicals, plant oxygenases represent a promising toolset for synthetic biologists to manipulate plant traits or develop biocatalysts (Harvey et al., 2015). Here, we review families of plant oxygenases and their chemistry and suggest potential applications.• Oxygenases can be used as a means to manipulate many facets of plant physiology. Alfieri A, Malito E, Orru R, Fraaije MW, Mattevi A (2008) Revealing the moonlighting role of NADP in the structure of a flavin-containing monooxygenase. Proc Natl Acad Sci USA 105: 6572-6577 Arnold FH (2018) Directed evolution: Bringing new chemistry to life.

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“…It is well known for its minimal redundancy, high quality of annotation, use of standardized nomenclature, and links to specialized databases. As Swiss-Prot is a protein sequence database, its repository contains the amino acid sequence, the protein name and description, taxonomic data, and citation information [39].…”

Section: Pirmentioning

confidence: 99%

Biological Databases- Integration of Life Science Data

Toomula¹,

Kumar²,

D³

et al. 2012

JCSB

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Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in biological information generated by the scientific community. Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analyses. Information contained in biological databases includes gene function, structure, localization, clinical effects of mutations as well as similarities of biological sequences and structures. This article presents information on some popular bioinformatic databases available online, including sequence, phylogenetic, structure and pathway, and microarray databases.

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Homology Modelling of Lycopene Cleavage Oxygenase: The Key Enzyme of Bixin Production

Cited by 5 publications

References 17 publications

Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase

Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase

Unleashing the Synthetic Power of Plant Oxygenases: From Mechanism to Application

Biological Databases- Integration of Life Science Data

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