Journal of PharmaSciTech Structural Insight of Homeobox DNA Binding Domain of Hox-B7A Protein of Esox lucius 1, 2 1 3 2,4 Subhamay Panda *, Leena Kumari , Subhra Prakash Hui and Santamay Panda Introduction Homeobox (Hox) genes are a set of transcription factors has been studied extensively in diverse fields of molecular and evolutionary biology. This protein family plays a very vital role in anterior-posterior axis patterning of animal embryos and in the development of tetrapod limb [1- 2]. The common feature of Hox proteins is the presence of 60 amino acids motif called homeodomain and Hox genes belong to the extensive superfamily of homeobox transcription factors [3]. The organisation of Hox genes within the genome in clusters is commonly found in several animals. A cluster of ancestral Hox gene, which is known to have originated from tandem duplications in early eukaryotic species, has been found in all bilaterian animals. Although Hox genes have diverged in various species but the homeodomain protein motif has remained highly conserved. Thus a given Hox gene can be easily assigned by means of homology to one of the genes along the cluster. Hox genes come under the category of one of the 14 known Paralogous Groups (PG). The duplication of ancestral cluster has been accomplished early in the vertebrate lineage [4-5]. In case of mammals, Hox genes are arranged in four clusters whereas teleost Hox genes are usually organised on 7 clusters, which resulted because of an additional duplication specific to teleost fishes [6-7]. The subsequent occurrence of lineage-specific gene has been affected, followed by diverse presence/absence combinations of Hox genes [8]. Hox genes encode a major group of evolutionarily conserved transcription factors controlling various functions such as axis specification and patterning of the central nervous system during embryonic development [9]. The Hox genes in vertebrates comprises of 13 paralog groups, expressed in the form of clusters on different chromosomes. In tetrapods, there are at least 39 genes are organized in 4 clusters, HoxA, HoxB, HoxC, and HoxD, whereas in teleosts, 4 clusters are found which resulted due to duplication of a whole genome early in their lineage [10-11]. The duplicated chromosomal regions are best exemplified by the occurrence of clusters of Hox genes [12-14]. Hox transcription factors are generally characterized by the presence of their DNA binding domain, the homeodomain. Hox genes were first discovered in the fruit fly Drosophila as the target gene for undergoing homeotic mutation, in which alteration in the segmental identity takes place, as in case of bithorax phenotype [15]. Hox genes are especially featured by their arrangement in the form of genomic clusters. A single cluster is found in all invertebrates that are either interrupted as in Drosophila species [16] or are found dispersed through the genome as in urochordates [17-18] and nematodes [19], whereas four clusters are a unique feature of the tetrapods such as human or frogs [8, 20], as akin to cartilaginous fish [21]. The invertebrates which are in close relation to vertebrates, such as the cephalochordate Branchiostoma [13, 22] possess a single cluster, which is also rearranged in case of the sea urchin [23]. The genome duplication in fish-specific genome resulted in the occurrence of seven Hox clusters in extant fish, with alternate cluster loss in Ostariophysi (HoxDb in zebrafish) [6] and Acanthopterygii (HoxCb in pufferfish, medaka, cichlid) [11, 24-25]. The additional clusters are not exactly alike to the homologous genes of tetrapods, but they usually undergoes independent losses of genes [8], thereby rendering much more variations in the gene content in teleost clusters than those of tetrapods. All of the fish species investigated till date experiences differences in gene content among their Hox clusters [8, 26-27]. The morphological variation and functional innovation relies upon the duplication of genes and entire genomes [12, 28-29]. During the evolution of the vertebrates, the clusters of Hox genes have experienced several rounds of duplication. Two rounds of genome duplication took place in case of jawed vertebrates, resulting in the production of four canonical Hox clusters of most gnathostomes designated as ''HoxA'', ''HoxB'', ''HoxC'', and ''HoxD'' clusters. In the case of subset of ray-finned fishes, a third round of Hox cluster duplication have been affected [6, 30-31] and forms seven to eight clusters referred to as ''Aa,'' ''Ab,'' etc. The objective of the present study is to evaluate the DNA binding domain of Homeobox protein Hox-B7a of Esox lucius (Northern pike) with reference to structure generation, validation of the generated models, distribution of secondary structural elements and positive charge distribution over the structure with the support of various bioinformatical algorithms. Abstract Homeobox (Hox) genes are important metazoan developmental genes they dictate the identity of embryonic regions along the anterio-posterior axis. A homeobox DNA binding region exists in homeobox protein Hox-B7a along the length of its sequence. The objective of the present study is to evaluate the DNA binding domain of Homeobox protein Hox-B7a of Esox lucius (Northern pike) with special reference to structure generation, validation of the generated models, distribution of secondary structural elements and positive charge distribution over the structure. With the use of comparative modeling approach to we propose the first 3D structure of DNA binding region of Hox-B7a Esox lucius. The current study focuses on the understanding of evolutionary structural enrichment strategy of DNA binding region of Hox-B7a. The appearance of different secondary structural element over structure provides for the molecule specific uniqueness of DNA binding region of Hox-B7a of Esox lucius. Keywords: Homeobox genes, Esox lucius, DNA binding region ISSN: 2231 3788 (Print) 2321 4376 (Online) Research Article 1 Department of Pharmacy, Gupta College of Technological Sciences, Ashram More, G.T. Road, Asansol-713301, India 2 Indian Institute of Human and Social Sciences, Sitarampur, Asansol-713359, India 3 Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool St, Darlinghurst, New South Wales 2010, Australia 4 Department of Physics, NSHM Faculty of Engineering & Technology, NSHM Knowledge Campus, Durgapur-713212, India *Correspondence: subhamay_panda@rediffmail.com, (Tel. +91 9531600015) http://www.pharmascitech.in 11 Volume 6, Issue 1, 2016; Journal of PharmaSciTech