Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling

Wang, Edina; Chinni, Suresh V.; Bhore, Subhash Janardhan

doi:10.6026/97320630010130

Cited by 3 publications

(2 citation statements)

References 33 publications

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“…[ 11 ] However, for the basic understanding of the gene (or its cDNA) structure, and secondary and tertiary structural features of the inferred proteins various computational tools and molecular modeling is commonly used. [ 12 13 14 ] In this study, the main goal was to annotate Pv AD gene cDNA and its deduced protein sequence. The Pv AD cDNA clone was isolated from 20 days old-pod tissue cDNA library, an indication of its expression in bean's 20 days old developing-pod-tissue.…”

Section: Discussionmentioning

confidence: 99%

Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein

Amelia¹,

Khor²,

Shah³

et al. 2015

Phcog Res

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Background:Common beans (Phaseolus vulgaris L.) are widely consumed as a source of proteins and natural products. However, its yield needs to be increased. In line with the agenda of Phaseomics (an international consortium), work of expressed sequence tags (ESTs) generation from bean pods was initiated. Altogether, 5972 ESTs have been isolated. Alcohol dehydrogenase (AD) encoding gene cDNA was a noticeable transcript among the generated ESTs. This AD is an important enzyme; therefore, to understand more about it this study was undertaken.Objective:The objective of this study was to elucidate P. vulgaris L. AD (PvAD) gene cDNA sequence and to predict the three-dimensional (3D) structure of deduced protein.Materials and Methods:positive and negative strands of the PvAD cDNA clone were sequenced using M13 forward and M13 reverse primers to elucidate the nucleotide sequence. Deduced PvAD cDNA and protein sequence was analyzed for their basic features using online bioinformatics tools. Sequence comparison was carried out using bl2seq program, and tree-view program was used to construct a phylogenetic tree. The secondary structures and 3D structure of PvAD protein were predicted by using the PHYRE automatic fold recognition server.Results:The sequencing results analysis showed that PvAD cDNA is 1294 bp in length. It's open reading frame encodes for a protein that contains 371 amino acids. Deduced protein sequence analysis showed the presence of putative substrate binding, catalytic Zn binding, and NAD binding sites. Results indicate that the predicted 3D structure of PvAD protein is analogous to the experimentally determined crystal structure of s-nitrosoglutathione reductase from an Arabidopsis species.Conclusions:The 1294 bp long PvAD cDNA encodes for 371 amino acid long protein that contains conserved domains required for biological functions of AD. The predicted deduced PvAD protein's 3D structure reflects the analogy with the crystal structure of Arabidopsis thaliana s-nitrosoglutathione reductase. Further study is required to validate the predicted structure.

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Section: Discussionmentioning

confidence: 99%

Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein

Amelia¹,

Khor²,

Shah³

et al. 2015

Phcog Res

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show abstract

“…[ 9 ] To understand the secondary and tertiary structural features of the proteins, molecular modeling is commonly used. [ 10 11 12 ] The main goal of this brief-study was to annotate Pv CaM gene cDNA and its deduced protein (amino acid) sequence. The Pv CaM cDNA clone was isolated from 5-day-old-pod tissue cDNA library; hence, it reflects that it is expressed in bean's 5-day-old developing-pod-tissue.…”

Section: Discussionmentioning

confidence: 99%

Analysis of common bean (Phaseolus vulgaris L., genotype BAT93) calmodulin cDNA using computational tools

Amelia¹,

Singh

Shah³

et al. 2015

Phcog Res

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Background:Common bean (Phaseolus vulgaris L.) is an important part of the human diet and serves as a source of natural products. Identification and understanding of genes in P. vulgaris is important for its improvement. Characterization of expressed sequence tags (ESTs) is one of the approaches in understanding the expressed genes. For the understanding of genes expression in P. vulgaris pod-tissue, research work of ESTs generation was initiated by constructing cDNA libraries using 5-day and 20-day old bean-pod-tissues. Altogether, 5972 cDNA clones were isolated to have ESTs. While processing ESTs, we found a transcript for calmodulin (CaM) gene. It is an important gene that encodes for a calcium-binding protein and known to express in all eukaryotic cells. Hence, this study was undertaken to analyse and annotate it.Objective:The objective of this study was to analyze and annotate P. vulgaris CaM (PvCaM) gene cDNA and its deduced protein (amino acids) sequence.Materials and Methods:Both strands of PvCaM cDNA clone were sequenced using M13 forward and reverse primer to elucidate the nucleotide sequence. The cDNA sequence and deduced protein sequence were analyzed and annotated using bioinformatics tools available online. The secondary structures and three-dimensional (3D) structure of PvCaM protein were predicted using the Phyre automatic fold recognition server.Results:Results showed that PvCaM cDNA is 818 bp in length. The cDNA analysis results showed that it contains an open reading frame that encodes for 149 amino acid residues. The deduced protein sequence analysis results showed the presence of conserved domains required for CaM function. The predicted secondary structures and 3D structure are analogous to the Solanum tuberosum CaM.Conclusions:This study analyzed and annotated PvCaM cDNA and protein. However, in order to obtain a complete understanding of PvCaM protein, further study on its expression, structure and regulation is essential.

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Molecular cloning and structural characterization of Ecdysis Triggering Hormone from Choristoneura fumiferana

Kumar

Viswanath

Devi

et al. 2016

International Journal of Biological Macromolecules

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Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling

Cited by 3 publications

References 33 publications

Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein

Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein

Analysis of common bean (Phaseolus vulgaris L., genotype BAT93) calmodulin cDNA using computational tools

Molecular cloning and structural characterization of Ecdysis Triggering Hormone from Choristoneura fumiferana

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