Practice question

Presence of L-arabinose triggers major structural rearrangement within AraC regulatory protein. Sugar molecule binds deep pocket within N-terminal domain forming hydrogen bonds that retract N-terminal arm from dimerization interface, altering interdomain orientation and allosteric communication. Dimer consequently loses high affinity for distal O2 site, abandons loop, and preferentially occupies adjacent half-sites araI1 centered minus 100 and araI2 at minus 50 directly upstream of PBAD promoter. Occupancy of I1-I2 positions AraC activation surface near minus45 facilitating direct interaction with sigma70 subunit and alpha C-terminal domain of RNA polymerase, breaking repressive loop and potently stimulating transcription initiation of araBAD catabolic genes.