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Fig. 4.

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Fig. 4. Phylogenetic tree and structure models of three DyPs expressed in Pseudomonas kribbensis CHA-19. (A) Phylogenetic analysis of the CHA-19 DyPs (TFH80052, TFH80975, and TFH81056). Multiple sequence alignment of the proteins was performed using ClustalW. The sequences represented by NCBI reference number were used for phylogenetic analysis. The phylogenetic tree construction from the aligned sequences was performed using MEGA 11. The phylogenetic tree was visualized using iTOL version 6. EfeB from Escherichia coli, PpDyP from Pseudomonas putida, and DyPB from Rhodococcus jostii RHA1 are shown as representative enzymes of the subclasses I3, P3, and P4, respectively. (B) Overall structure of the CHA-19 DyPs predicted by ColabFold platform. Left, predicted multimer structure of each protein; middle, superimposition of the predicted DyPs structures with their corresponding proteins, EfeB (PDB ID: 3O72), PpDyP (PDB ID: 7QYQ), and DyPB (PDB ID: 3QNS); right, zoom-in view of the heme active site. The heme site structures are shown as stick and sphere models. The water molecule is depicted as a cyan sphere. The active site residues have hydrogen bond interaction with heme molecule in PDB data of DyPs.
J. Microbiol. Biotechnol. 2024;34:1867~1875 https://doi.org/10.4014/jmb.2406.06021
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