Structural Model Comparison of Histidine Decarboxylase (Hdc) of Histamine-Producing Bacteria Morganella Morganii Constructed by Alphafold2 and Swissmodel

Morganella morganii is one of bacteria that is capable of converting histidine to histamine in fishery products, particularly of the histidine-rich species Scobridae family.The enzyme responsible for the conversion of histidine to histamine is histidine decarboxylase (HDC), however the crystal structure of Morganella morganii HDC has not been reported.The aim of this study was to compare HDC structure models of Morganella morganii constructed de novo with AlphaFold2 and by homologous modeling with SwissModel.The overall structure of both models showed a high similarity with the superposition of α-backbone of both models (R.M.S.D.) being 0.522 Å.The active site analysis shows the position of Lys233, which can form an internal aldimine (Lys-pyridoxal-5'-phosphate) in both conservation models with Lys233 HDC from Photobacterium phosphoreum (PDB 7ERV).The main difference between the two models lies in the Asp252-Val256 residues, which form an α-helix in the AlphaFold2 model, while these residues form a loop in the SwissModel model and the P. phosphoreum HDC crystal structure.Nevertheless, the putative structure model of HDC from Tetragenococcus halophilus with a low level of amino acid sequence homology shows a different structure with an R.M.S.D reaching 1.103 Å.This research shows that modeling for HDC proteins with a high level of amino acid sequence similarity can be performed using de novo and homologous modeling methods.