In silico analysis of some microbial amidases for their amino acid and physiochemical parameters

Krishan Gopal, Nikhil Sharma, Tek Chand Bhalla*

Abstract


Amino acid sequences of amidases were retrieved from respective databases and in silico analysis for different physiochemical properties and substrate specificity has been done. Multiple Sequence Alignment (MSA) and statistical analysis of amino acid sequences has revealed significant differences among aliphatic and signature amidases in terms of conserved motif that plays a vital role in substrate binding and catalytic function. MSA has revealed that in aliphatic amidases the conserved amino acid residues involved in catalytic function are position specific which remains within catalytic traid of Cys-166, Glu-59, Lys-134, while signature amidase contains signature motif GGSS (S/G) GS and catalytic traid of Ser-171, Ser-195, Lys-96 which are not position specific. Statistical analysis has revealed that these two groups also differ in physiochemical properties. In contrast to aliphatic amidases, signature amidase have significantly higher number of amino acid residues & molecular mass, theoretical pI, charged (negative and positive) residues, aliphatic index and grand average of hydropathicity. Present investigation revealed that the amino acid residues i.e. Cys, Met, Tyr, Asn, Ile, Trp, Glu and Gly in aliphatic amidases, while in case of signature amidases amino acids i.e Leu, Pro, Ser, Ala and Val have been found to play an important and significant role both in enzyme catalysis, substrate specificity as well as in structural stability.

Keywords


Amidase; Aliphatic amidase; Signature amidase; Amino acid; Substrate specificity; Multiple alignments.

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References


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DOI: http://dx.doi.org/10.21746/ijbio.2013.04.0012

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