Journal of
Medical Genetics and Genomics

  • Abbreviation: J. Med. Genet. Genomics
  • Language: English
  • ISSN: 2141-2278
  • DOI: 10.5897/JMGG
  • Start Year: 2009
  • Published Articles: 48

Full Length Research Paper

In silico analysis of the two forms of lysine decarboxylase

Gokulnath Krithika and Namasivayam Gautham*
Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy campus, Chennai- 600 025, India.
Email: [email protected]

  •  Accepted: 18 July 2010
  •  Published: 31 December 2010


Amino acid decarboxylases are expressed in response to acidic pH in bacteria. Among amino acid decarboxylases, lysine decarboxylase is expressed to levels constituting 2% of the total cell protein during acid stress. In bacteria, two forms of lysine decarboxylase exist, namely the inducible CadA and the constitutively expressed Ldc. The two proteins catalyse the conversion of lysine to cadaverine as an acid tolerance response. Here, we report the in silico analysis of these two sequences in an attempt to identify the differences between the two proteins and the reason for the existence of the two variants. The analysis showed that the two proteins could be differentiated on the basis of the amino acid composition, and the organisation of sequence motifs. The two forms of lysine decarboxylase were found to segregate into different branches in phylogenetic analysis. Sequence comparison with other amino acid decarboxylases showed that most of the motifs are conserved among pyridoxal phosphate binding amino acid decarboxylases. 

Key words: Lysine decarboxylase, inducible form(cadA),constitutive form(Ldc),acid tolerance, motif analysis, phylogenetic analysis, virulence, conserved sequence motifs, pyridoxal phosphate binding enzyme, amino acid decarboxylase, gamma proteobacteria, PCA, cluster analysis, functional annotation.