<p>Maintaining carbon/nitrogen (C/N) metabolic balance is essential for cellular homeostasis, allowing microorganisms to adapt to fluctuating environmental conditions. In the autotrophic cyanobacteria, the C/N balance is achieved through a sophisticated network that coordinates the uptake of inorganic carbon and nitrogen, including the ATP-binding cassette&#xa0;(ABC) transporters CmpABCD and NRT that import bicarbonate and nitrate, respectively. Notably, both transporters possess an extra C-terminal regulatory domain (CRD) that is fused to one of the nucleotide-binding domains (NBDs). Via structure guided site-directed mutagenesis and bicarbonate transport activity assays, we found that CmpABCD is tightly regulated by the nitrate-binding CRD. At a low intracellular nitrate concentration, CmpBCD adopts an auto-inhibited conformation, in which the CRD locks the two NBDs of CmpC and CmpD. Upon binding to the nitrate, the CRD is released from NBDs and becomes highly flexible, thus restoring the transport activity of CmpABCD. We propose a distinct regulatory mechanism of ABC transporters, which may be broadly applicable to those fused with a regulatory domain. Moreover, these findings combined with previous reports establish a direct link between the inorganic carbon uptake and intracellular nitrate level through an ABC importer, providing a straightforward and economic strategy that coordinates the C/N homeostasis.</p>