Wallace Richardson, 64, was behind the wheel of the bus the morning of July 14 when it crashed at Octavia Boulevard and Oak Street. The crash killed Dr. Kevin Mack.
The shuttle bus was carrying about 15 people when Richardson allegedly entered the intersection on a red light and struck a big-rig, causing Mack to be ejected from the vehicle, prosecutors said. Mack was pronounced dead at the scene.
A warrant was issued for Richardson's arrest in December, and he turned himself in to Millbrae police last month.
After entering his plea, Richardson was ordered to return to court on March 7 for a pretrial conference in the case, according to the district attorney's office.
