In Silico Structural Characterization of Monooxygenase and Dioxygenase Enzymes from Danio Rerio

Int. J. of Life Sciences, 2017, Vol. 5 (4): 570-576 ISSN: 2320-7817| eISSN: 2320-964X RESEARCH ARTICLE In silico structural characterization of Monooxygenase and dioxygenase enzymes from Danio rerio Chittaranjan Baruah1,* and Papari Devi2 1Department of Zoology, Darrang College, Tezpur – 784001, Assam, India 2Department of Zoology, Kaliabor College, Kuwarital-782137, Assam, India *Corresponding author: [email protected] Manuscript details: ABSTRACT Received: 05.10.2017 Freshwater fish having both retind and dehydretind showed the capabilities Accepted: 01.12.2017 of clearing the provitamin A-Status carotenoids into both forms of Vitamin Published : 05.12.2017 A, either through central or terminal cleavage. The involvement of monooxygenase and dioxygenase enzymes system has been identified. The Editor: Dr. Arvind Chavhan present manuscript is presenting an in silico analysis that has been Cite this article as: performed for molecular modeling and functional annotation of Chittaranjan Baruah and Papari Devi Monoxygenase and Dioxygenase enzymes from Danio rerio using sequence (2017) In silico structural data extracted from publicly available database. The functional annotations characterization of Monooxygenase have been performed using several publicly available Bioinformatics tools and Dioxygenase enzymes from and databases. The study represents the application of comparative Danio rerio; International J. of Life modeling method for 3D structure prediction. The functional annotations Sciences, 5 (4): 570-576. have been performed using several publicly available Bioinformatics tools and databases. Acknowledgement The paper is dedicated with deep reverence to Late Professor UC Keywords: Beta-carotene, Vitamin A, Homology modelling, phylogeny, Goswami, Former Professor and ortholog, paralog Head of Department of Zoology, Gauhati University, Assam, India who inspired the authors for molecular INTRODUCTION and in-silico analysis of Retinoids and Carotinoids. Retinoids play an essential role in vision, cell differentiation, embryonic development, membrane and skin protection and are crucial for the health Copyright: © 2017| Author (s), This of mammals and other vertebrates. Retinoids are obtained from provitamin is an open access article under the terms of the Creative Commons A carotenoids, like β-carotene, through the oxidative cleavage by β-carotene Attribution-Non-Commercial - No 15, 15′ monooxygenase enzyme. It belongs to an extended family of Derivs License, which permits use dioxygenases which include the plant neoxanthin cleavage enzymes, the and distribution in any medium, bacterial lignostilbene dioxygenases, and the vertebrate protein RPE65. provided the original work is Members of this family interact with carotenoids and other polyenes properly cited, the use is non- (Redmond et al., 2001). commercial and no modifications or adaptations are made. The mechanism of the formation of Vitamin A has been studied since 1930(March, 1930, 1957) and several workers has identified the involvent of both monooxygenase and dioxygenase enzyme catalyzing the clearing process of B-carotene and others either centrally or terminally stepwise following B- oxidation (Barua and Goswami, 1977). We have reported the © 2017 |IJLSCI www.ijlsci.in 570 In silico structural characterization of Monooxygenase and Dioxygenase enzymes from Deneo rerio metabolism of B-carotene, lutein, astaxanthin and of 1e-05 with 23.8 % identity and 520 overlap in the cryptoxanthin in both retinoid-rich as well as BLAST result. The target-template alignment and dehydroretind-rich fish. Considering the involvement model building were conducted manually by using of dioxygenase and mono-oxygenase system in Modeller program (Marti-Renom et al., 2000). The ab- clearing the caronotenoids molecules in the above initio loop modeling was conducted by MODLOOP mentioned pesitien, the structure of the enzymes has server. The final 3D structures with all the coordinates been elucidated as described in Zebra fish, Danio rerio. for both the targets were obtained by optimization of a D. rerio is widely distriunted freshwater fish of the molecular probability density function (pdf) of cyprinidae, which is rich in retind (75%) and Modeller as well as MODLOOP (Eswar et al., 2006). dehydroretind (25%) (Barua et al., 1973; Goswami The 3D structures were evaluated (Giorgetti et al., and Baruah, 1981). 2005) by ProCheck (Laskowski et al., 2003). After fruitful verification of the coordinate files, the Although there is an availability of sequence structures were successfully deposited to PMDB for information for monooxygenase and dioxygenase the access to the scientific community (Tiziana et al., enzymes from Danio rerio, yet there is no structural 2006). All the graphic presentations of the 3D information and functional annotation available. structures were prepared using Chimera (Pettersen et Therefore, the biochemistry and molecular mechanism al., 2004). of their functions are still not very well understood. The present study was carried out to predict the 3D C. Sequence based functional annotation folding pattern (Zemla et al., 1999), sequence based The sequence based functional annotation have been functional annotation of monooxygenase and carried out for dioxygenase and monooxygenase dioxygenase enzymes from Danio rerio and their enzymes of 536 sequences from 204 different species sequence variation to identify their structural and in the sequence database, using Pfam evolutionary properties in order to characterize the (pfam.sanger.ac.uk/), GO (www.geneontology.org/), role of the two enzyme in fish model. KEGG database (www.genome.jp/kegg/). Orthologs paralogs have been identified and details given in the phyologenetics analysis. MATERIALS AND METHODS a. Beta-carotene 15, 15-monooxygenase 2 KEEG ID: A. Acquisition and alignment of sequences dre: dre:84039. The sequences of Danio rerio monooxygenase and Gene ontology shows the monooxygenase activity dioxygenase enzymes were acquired from the through catalysis of the incorporation of one atom UniProtKB (Accession no. Q1RLW1 and Q7ZTS0 from molecular oxygen into a compound and the respectively). The significance of the BLAST results reduction of the other atom of oxygen to water. was assessed by expect values (e-value) generated by BLAST family of search algorithm (Altschul et al., b. Beta-carotene 15, 15-dioxygenase 2 : KEEG ID: 1991). ClustalW analysis software available online dre:678554 from EBI was used to compare sequence alignment of Oxidoreductase activity, acting on single donors with monooxygenase and dioxygenase enzymes incorporation of molecular oxygen, incorporation of (www.ebi.ac.uk/clustalw/). Default settings were used two atoms of oxygen. (From Gene ontology database.) except that a gap extension setting of 3 was used. ClustalW results were illustrated using Boxshade v3.21(http://www.ch.embnet.org/software/BOX_for RESULTS AND DISCUSSION m.html). The predicted 3D Structures B. Three-dimensional structure prediction The models of monooxygenase and dioxygenase For Comparative (Homology) modeling,the 3D enzymes from Danio rerio have been deposited to coordinates of of pdb ID 2BIW Chain A (Crystal PMDB with the assignment unique PMDB IDs structure of apocarotenoid cleavage oxygenase from PM0075185 and PM0075184 respectively (Figures 1,2 synechocystis, native enzyme with ) have been &3) for the coordinate entry. The structure of choosed as the suitable template which shows E-value Monooxygenase has 371 H-bonds, 6 helices, 51 strands www.ijlsci.in Int. J. of Life Sciences, Vol. 5(4) December 2017 571 Chittaranjan and Papari, 2017 and 68 turms while the structure of Dioxygenase has good quality as judged by Ramachandran Plot 403 H-bonds, 6 helices, 55 strands and 62 turns. (Ramachandran & Sasisekharan, 1968). Procheck verification proved that the models are of Figure 1. The Theoretical models. A. Beta-carotene 15, 15’-monooxygenase 1 (PM0075185) and B. Beta- carotene 15, 15-dioxygenase 2 (PM0075184), displayed by UCSF Chimera. Figure 2. The secondary structure information of Beta-carotene 15, 15’-monooxygenase 1 (PM0075185). 572 Int. J. of Life Sciences, Vol. 5(4) December, 2017 In silico structural characterization of Monooxygenase and Dioxygenase enzymes from Deneo rerio Figure 3. The secondary structure information of Beta-carotene 15, 15-dioxygenase 2 (PM0075184). Functional annotation a. Beta-carotene 15,15'-monooxygenase 1 b. Beta-carotene 15, 15-dioxygenase 2 Catalysis of the incorporation of one atom from Oxidoreductase activity, acting on single donors with molecular oxygen into a compound and the reduction incorporation of molecular oxygen, incorporation of of the other atom of oxygen to water. (From Gene two atoms of oxygen. (From Gene ontology database; ontology database.). Figures 4 & 5). www.ijlsci.in Int. J. of Life Sciences, Vol. 5(4) December 2017 573 Chittaranjan and Papari, 2017 Figure 4. Clefts and cavities in protein structure, Beta-carotene 15,15'-monooxygenase 1 the colours corresponding to the entries in the table below. Figure 5. Clefts and cavities in protein structure, Beta-carotene 15, 15-dioxygenase 2 the colours corresponding to the entries in the table below Fig. 4 Fig. 5 Fig. 4 * Residue-type colouring: Positive Negative Neutral Aliphatic Aromatic Pro & Gly Cysteine H,K,R D,E S,T,N,Q A,V,L,I,M F,Y,W P,G C * Colouring by residue-conservation score: blue purple skyblue cyan grey green yellow orange pink Red 0.0-0.1 0.1-0.2 0.2-0.3 0.3-0.4 0.4-0.5 0.5-0.6 0.6-0.7 0.7-0.9 0.8-0.9

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