Molecular mechanism of the alkyl-transferase MtaA catalyzing butyl-CoM in the thermophilic butane-oxidizing archaea Candidatus Syntrophoarchaeum

Abstract:

[Background] Thermophilic archaea Candidatus Syntrophoarchaeum was found to coexist with sulfate-reducing bacteria and oxidize n-butane by the reverse methanogenesis pathway. However, in this process, the enzyme responsible for catalyzing the oxidation of butyl-CoM has not been determined yet. [Objective] Using molecular dynamics simulation to prove that the enzymes encoded by mtaA genes found in Ca. Syntrophoarchaeum can specifically catalyze the transfer of butyl in butyl-CoM, and they are not methyltransferases. [Methods] Using the crystal structure of Methanosarcina mazei coenzyme M methyltransferase MtaA (PDB ID:4ay8) as a template, homology modeling of MtaA_1 (GenBank ID:OFV65993.1) and MtaA_2 (GenBank ID:OFV65678.1) was performed. Molecular docking was used to obtain the structure when they were combined with CH₃-CoM and C₄H₉-CoM respectively, and AMBER18 was used for molecular dynamics simulation. [Results] When combined with C₄H₉-CoM, MtaA_1 and MtaA_2 exhibited a TIM-barrel-like three-dimensional structure similar to the fold of 4ay8. However, there are differences in the shape of the active site, the distance between Zn²⁺ and the substrate, and the coordination of amino acid residues around the active site. These differences may be the reason why the enzymes encoded by mtaA genes found in Ca. Syntrophoarchaeum catalyze the oxidation of butyl-CoM. The overall structure of MtaA_2 is more similar to 4ay8, and the coordination of residues around the active site is complete, suggesting that MtaA_2 is more likely to be active. When MtaA_1 and MtaA_2 bind to CH₃-CoM respectively, their overall structures are unrealistic, and the coordinated Zn²⁺ is too far away from the substrate, indicating that CH₃-CoM is almost impossible to bind to the enzyme. [Conclusion] MtaA_1 and MtaA_2 of Ca. Syntrophoarchaeum are likely to be specific butyl-transferases rather than catalyzing the transfer of methyl groups, and MtaA_2 is more likely to be active.