Structural analysis of catalase from two Musa accessions, FHIA18 and Williams, and from Ravenala madagascariensis.
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.
Khoyratty
Sher-ullah S S
SU
Faculty of Agriculture, University of Mauritius, Mauritius.
Souza
Manoel T
MT
Jaufeerally-Fakim
Yasmina
Y
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002374:Catalase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D003198:Computer Simulation; D017124:Conserved Sequence; D006861:Hydrogen Peroxide / Q000737:chemistry / Q000378:metabolism; D021621:Imaging, Three-Dimensional; D008958:Models, Molecular; D008969:Molecular Sequence Data; D028521:Musa / Q000145:classification* / Q000201:enzymology* / Q000235:genetics; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D032428:Strelitziaceae / Q000201:enzymology* / Q000235:genetics; D040681:Structural Homology, Protein; D031064:Zantedeschia / Q000201:enzymology / Q000235:genetics
D006861:Hydrogen Peroxide; D002374:Catalase