Homology Modeling and Comparative Profiling of Superoxide Dismutase Among Extremophiles: Exiguobacterium as a Model Organism

Superoxide dismutase (SOD), a well known antioxidant enzyme, is known to exert its presence across bacteria to humans. Apart from their well-known antioxidant defense mechanisms, their association with various extremophiles in response to various stress conditions is poorly understood. Here, we have...

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Bibliographic Details
Published in:Indian journal of microbiology 2014-12, Vol.54 (4), p.450-458
Main Authors: Pathak, Rajiv, Narang, Pankaj, Chandra, Muktesh, Kumar, Raj, Sharma, P. K, Gautam, Hemant K
Format: Article
Language:English
Subjects:
amino acid sequences
Amino acids
Antioxidants
bacteria
Biomedical and Life Sciences
consensus sequence
defense mechanisms
Deinococcus radiodurans
energy
Enzymes
Exiguobacterium
extremophiles
humans
Life Sciences
Ligands
Medical Microbiology
Microbiology
Microorganisms
Original
Original Article
Oxidative stress
Phylogenetics
phylogeny
Physicochemical properties
Prokaryotes
Radiation
Standard scores
superoxide dismutase
Thermus thermophilus
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Summary:Superoxide dismutase (SOD), a well known antioxidant enzyme, is known to exert its presence across bacteria to humans. Apart from their well-known antioxidant defense mechanisms, their association with various extremophiles in response to various stress conditions is poorly understood. Here, we have discussed the conservation and the prevalence of SODs among 21 representative extremophiles. A systematic investigation of aligned amino acid sequences of SOD from all the selected extremophiles revealed a consensus motif D-[VLE]-[FW]-E-H-[AS]-Y-[YM]. To computationally predict the correlation of SOD with the various stress conditions encountered by these extremophiles, Exiguobacterium was selected as a model organism which is known to survive under various adverse extremophilic conditions. Interestingly, our phylogenetic study based on SOD homology revealed that Exiguobacterium sibiricum was one of the closest neighbors of Deinococcus radiodurans and Thermus thermophilus. Next, we sought to predict 3-D model structure of SOD for E. sibiricum (PMDB ID: 0078260), which showed >95 % similarity with D. radiodurans R1 SOD. The reliability of the predicted SOD model was checked by using various validation metrics, including Ramachandran plot, Z-score and normalized qualitative model energy analysis score. Further, various physicochemical properties of E. sibiricum SOD were calculated using different prominent resources.
ISSN:0046-8991
0973-7715
DOI:10.1007/s12088-014-0482-8