Oxygenases and methods of biologically upgrading hydrocarbon streams, such as crude oil, using oxygenases are provided herein. The oxygenases can be used to remove impurities such as metals, heteroatoms, or asphaltenes from a hydrocarbon stream. In some cases, the oxygenases can be chemically or genetically modified and can be used in different locations such as petroleum wells, pipes, reservoirs, tanks and/or reactors.