We used various servers and softwares to analyze the sequences and to predict the three dimensional structure and function of the Homogentisate-1,2-dioxygenase. In the present study Sequence, Structural and Functional Characterization of Homogentisate-1,2-dioxygenase of Homo sapiens: An in silico analysis. Therefore, it is very interesting as well as important to carry out the study of Homogentisate-1,2-dioxygenase of Homo sapiens. Plenty of work has been done on Homogentisate - 1, 2 -dioxygenase of various organisms.The Protein Data Bank (PDB) (contain very little information about three dimensional structure of Homogentisate - 1, 2 - dioxygenase of Homo sapiens. This epoxide intermediate allowing radical reactions to eventually open and oxidize the six-membered ring. In the next step, O 2 is cleaved with the formation of an epoxide. O 2 then binds to the iron atom, subsequently reacting with the aromatic ring to form a peroxo-bridged intermediate. The iron atom is also coordinated to His335, His371, and Glu341. In the first two steps Fe 2+ coordinates to the carbonyl and ortho phenol oxygens. propose a mechanism for HGD which is The opening of the aromatic ring in homogentisate is a multi-step process. The active site of Homogentisate 1,2-dioxygenase was determined through the crystal structure, which was captured through the work of Titus et al. The other effect of the ochronotic pigment is that it can accumulate in the body’s connective tissue leading to degenerative arthritis, as the person grows older. This first of these effects is that the patient’s earwax will begin to turn black or red, depends on the patient’s diet, since the blood becomes oxidized and thus turns black due to excess of the ochronotic pigment. AKU is due to the inability of the body to deal with homogentisate, which when oxidized by the body will produce the compound known as the ochronotic pigment. HGD requires the use of Fe 2+ and O 2 in order to cleave the aromatic ring of homogentisate. Homogentisate reacts with HGD to produce maleylacetoacetate, which then is further used in the metabolic pathway. Homogentisate 1,2-dioxygenase is involved in the catabolism of aromatic rings, more specifically in the breakdown of the amino acids tyrosine and phenylalanine.HGD appears in the metabolic pathway of tyrosine and phenylalanine degradation when homogentisate is produced. An absence or deficiency of homogentisate-1,2-dioxygenase will result in alkaptonuria (AKU). Introduction Homogentisate-1,2-dioxygenase (HGD) is an iron containing enzyme which catalyzes the conversion of homogentisate to 4-maleylacetoacetate. This study highlights the sequence, structural and functional information of the protein.ġ. The function of the protein is predicted and analyzed. Fold of the protein and motif of the protein is also predicted. Active site of the structure, Protein disorder, disorder propensity and Average Area Buried Upon Folding is also predicted and analyzed. The model generated for Homogentisate-1,2-dioxygenase is successfully submitted to the Protein Model Database (PMDB) having PMID PM0079008. Energy minimization, Refinement and validation of the structure is done, which suggest the structure to be a very good quality. 3D structure of the protein is predicted and characterized. Sub cellular localization prediction suggested that all of the sequences are secretory without transit peptide. Secondary structure analysis shows that all of the sequences of Homogentisate-1,2-dioxygenase have predominant sheet and random coil structure. The aliphatic index computation infers that Homogentisate-1,2-dioxygenase of homo sapiens can’t tolerate wide range of temperature.
Primary structure analysis reveals that all the six sequences of Homogentisate-1,2-dioxygenase arehydrophobic in nature (due to the high content of non- polar residues) without transmembrane region. So, the present study has been undertaken to carried out in silico prediction of structure and function of Homogentisate-1,2-dioxygenase of homo sapiens. It is most significant and helpful when very little information about three dimensional (3D) structure of protein(uncharacterized) available in the Protein Data Bank (PDB). In silico characterization and molecular modeling of a protein opens wide scope for the prediction of structural and functional information.
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