Heh, it always amazes me the # of people who come on the board to ask questions that obviously indicate that they aren't using the Arduino framework at all. Anyway, looking at the Arduino core library source would help here:
Here is the code that Arduino uses to initialize a UART:
// Configure PMC
pmc_enable_periph_clk( _dwId ) ;
// Disable PDC channel
_pUart->UART_PTCR = UART_PTCR_RXTDIS | UART_PTCR_TXTDIS ;
// Reset and disable receiver and transmitter
_pUart->UART_CR = UART_CR_RSTRX | UART_CR_RSTTX | UART_CR_RXDIS | UART_CR_TXDIS ;
// Configure mode
_pUart->UART_MR = UART_MR_PAR_NO | UART_MR_CHMODE_NORMAL ;
// Configure baudrate (asynchronous, no oversampling)
_pUart->UART_BRGR = (SystemCoreClock / dwBaudRate) >> 4 ;
// Configure interrupts
_pUart->UART_IDR = 0xFFFFFFFF;
_pUart->UART_IER = UART_IER_RXRDY | UART_IER_OVRE | UART_IER_FRAME;
// Enable UART interrupt in NVIC
NVIC_EnableIRQ(_dwIrq);
// Enable receiver and transmitter
_pUart->UART_CR = UART_CR_RXEN | UART_CR_TXEN ;
You'll notice that you do need to enable the clock first.