Quarterback Alex Smith is staying with the San Francisco 49ers after agreeing today to a restructured contract sharply reducing his base salary.

The former No. 1 overall draft pick was due to make nearly $10 million in the upcoming season under the contract he signed in 2005. Financial terms weren't immediately available, but the 49ers now have Smith under contract for the next two years at a salary more commensurate with his four up-and-down seasons with the club.

"Alex expressed a deep interest to remain with the team, and that feeling was mutual," said 49ers general manager Scot McCloughan, who would have released Smith before training camp without a reworked deal.

The deal allows Smith to join the 49ers on Monday for their first offseason team meetings and a minicamp on the weekend under Jimmy Raye, San Francisco's fifth offensive coordinator in Smith's five seasons. Smith couldn't have participated in the workouts without a new contract because of insurance liabilities.

Smith missed most of the past two seasons with injuries while feuding with former coach Mike Nolan. After Mike Singletary replaced Nolan midway through last season, Smith became more outspoken about his desire to stay in San Francisco.

Smith, whose recent honeymoon delayed negotiations on his new deal, is still hoping to live up to the promise that compelled the 49ers to choose him at the top of the notoriously flimsy 2005 draft ahead of Aaron Rodgers, Braylon Edwards, DeMarcus Ware and Shawne Merriman.

The 49ers still believe the former Utah star has potential he hasn't tapped after just one full season as their starter, in 2006. Smith has passed for 4,679 yards in 32 career games, throwing 19 touchdown passes and 31 interceptions.

Smith separated his throwing shoulder in the fourth game of 2007 on a sack by Seattle's Rocky Bernard. He attempted to return quickly from the injury, but his struggles opened a rift with Nolan, with each accusing the other of misunderstanding the injury.

Smith underwent shoulder surgery after the season, but then broke a bone elsewhere in his shoulder. He didn't play at all last season, undergoing more surgery in October to clean up his shoulder.

After the 49ers failed in their pursuit of free agent quarterback Kurt Warner last week, Smith is expected to head into training camp in competition for the starting job with Shaun Hill, who is 7-3 as a starter over the past two seasons. San Francisco also signed veteran quarterback Damon Huard last week.

Raye is the 49ers' seventh offensive coordinator in seven seasons overall, and the annual installation of a new scheme has led to offenses that were the NFL's worst in two of Smith's four seasons.