We have generated 3 ns molecular dynamic (MD) simulations, in aqueous solution, of the bacterial soluble glucose dehydrogenase enzyme-PQQ-glucose complex and intermediates formed in PQQ reduction. In the MD structure of enzyme-PQQ-glucose complex the imidazole of His144 is hydrogen bonded to the hydroxyl hydrogen of H-OC1(H) of glucose. The tightly hydrogen-bonded triad Asp163-His144-glucose (2.70 and 2.91 Angstrom) is involved in proton abstraction from glucose concerted with the hydride transfer from the C1-H of glucose to the > C5=O quinone carbon of PQQ. The reaction is assisted by Arg228 hydrogen bonding to the carbonyl oxygen of >C5=O. The rearrangement of -(H)C5(O-)-C4(=O)- of II to -C5(OH)=C4(OH)- of PQQH(2) hydroquinone is assisted by general acid protonatation of the >C4=O oxygen by protonated His144 and hydrogen bonds of Arg228 to the oxyanion O5. The continuous hydrogen bonding of the amide side chain of Asn229 to >C4=O4 oxygen and that of the 05 oxygen of the cofactor to Wat89 is observed throughout the entire reaction.