Cystathionine β-Lyase-Like Protein with Pyridoxal Binding Domain Characterized in Leishmania major by Comparative Sequence Analysis and Homology Modelling
Cystathionine β-lyase-like protein (CBLP), one of the key enzymes involved in methionine biosynthesis utilising pyridoxal phosphate (PLP) as a cofactor, has recently been reported in Leishmania major. Its presence in the parasite and absence in humans warrant its full characterisation and fruition as a potent, selective, and inevitable druggable target. Due to the unavailability of X-ray 3D structure of CBLP, a homology model for this protein was developed for the first time. The model was evaluated for PLP binding site and various conserve domain residues of the protein recommended by comparative sequence analyses by different protein analysis tools. The model was validated and discovered to be robust and statistically significant. The final model was superimposed on template of Arabidopsis thaliana (PDB ID: 1IBJ) and RMSD was found to be 0.486. The PLP binding site residues of both the proteins were ensued to be highly conserved indicated by Gly71, Met72, Tyr95, Asp169, and Ser193 as well as formation of aldimine bond with Lys194. This was further verified through molecular simulation of PLP into the cofactor binding site of the modelled protein. The present study may therefore play a directing role in the designing of novel, potential, and selective antileishmanial agents. 1. Introduction Cystathionine β-lyase (CBL, EC 4.4.1.8) found in plants and microbes is a pyridoxal-5′-phosphate (PLP)-dependent homotetrameric enzyme of approximately 35–40？kDa and catalyses the penultimate step of methionine biosynthesis, that is, α, β-elimination reaction, where cystathionine is hydrolysed into pyruvate, ammonia, and homocysteine (Figure 1) [1, 2]. Subsequently, homocysteine gets methylated to methionine. The overexpression of CBL encoding metC gene in D-alanine gene knockout models of several bacteria was found to be significant for their sustenance in host cell environment [3]. In addition, CBL also dictated the virulence of Salmonella enterica [4] thus playing a decisive role in its pathogenicity. Although, in 2007, Ejim et al. explored CBL as a drug target in bacteria [5], its role in protozoan is yet to be delved into. Figure 1: Metabolism of cystathionine by cystathionine β-lyase. Recently, the decoding of the Leishmania genome [6, 7] facilitated in extracting significant information regarding the presence of a new homolog of CBL, cystathionine β-lyase-like protein (CBLP), a 50？kDa translated peptide of 459 amino acids which shares 48.05% structural resemblance with CBL of Arabidopsis thaliana. This information also revealed that 64–447 amino acids make up
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