Affiliations: Faculty of Agriculture, University of Mauritius,
Mauritius | Embrapa LABEX, Europa Plant Research International
(PRI), Wageningen University & Research Centre (WUR), The
Netherlands
Abstract: Nucleotide sequences of catalase were obtained following
amplification using specific primers and were blasted against Musa
acuminata catalase 2 mRNA from NCBI (157418810). Clustering of the amino acid
sequences from NCBI was done using Clustal X. The latter revealed that FHIA18
catalase is more related to Ravenala madagascariensis (Musa
relative) catalase while the Williams catalase is more related to a clade
containing a Musa acuminata (Musa ancestor) catalase from NCBI. The
tertiary structures and the catalase consensus functional sites, based on the
Pseudomonas syringae catalase structural template, were obtained for
FHIA18, Williams, Ravenala madagascariensis and Musa acuminata
catalases. They were found to differ slightly. Using known features of
catalase active sites, four pre-requisite criteria were defined to find such
sites: (1) Position of tyrosine axial to heme determined by X-ray diffraction,
(2) 7 conserved amino acids in the active site found by sequence alignment, (3)
favourable docking energy, and (4) presence of an unobstructed long tunnel that
leads the ligand to the active site. Two differing potential docking sites were
found for both FHIA18 and Williams that fit a maximum number of criteria. In
terms of 1D sequence, the region of the docking site for Williams is within the
catalase domains as seen upon NCBI blast. The counterpart of FHIA18 for the
same region is not. This sequence difference between FHIA18 and Williams
affects the best docking site in FHIA18 and Williams in silico.
Keywords: Catalase, conserved, clustering, active sites, pockets, tunnels, docking
