In Gram-positive bacteria, the catabolite control protein A (CcpA) functions as the master transcriptional regulator of carbon catabolite repression/regulation (CCR). To effect CCR, CcpA binds a phosphoprotein, either HPr-Ser 46 -P or Crh-Ser 46 -P. Although Crh and histidine-containing protein (HPr) are structurally homologous, CcpA binds Crh-Ser 46 -P more weakly than HPr-Ser 46 -P. Moreover, Crh can form domain-swapped dimers, which have been hypothesized to be functionally relevant in CCR. To understand the molecular mechanism of Crh-Ser 46 -P regulation of CCR, we determined the structure of a CcpA-(Crh-Ser 46 -P)-DNA complex. The structure reveals that Crh-Ser 46 -P does not bind CcpA as a dimer but rather interacts with CcpA as a monomer in a manner similar to that of HPr-Ser 46 -P. The reduced affinity of Crh-Ser 46 -P for CcpA as compared with that of HPr-Ser 46 P is explained by weaker CrhSer 46 -P interactions in its contact region I to CcpA, which causes this region to shift away from CcpA. Nonetheless, the interface between CcpA and helix ␣2 of the second contact region (contact region II) of Crh-Ser 46 -P is maintained. This latter finding demonstrates that this contact region is necessary and sufficient to throw the allosteric switch to activate cre binding by CcpA.
Carbon catabolite repression/regulation (CCR)2 is a global regulatory mechanism utilized by bacteria to select, out of a mixture of compounds, the carbon source providing the optimal growth advantage (1-3). CCR is mediated largely at the level of transcription. The master transcriptional regulator of CCR in bacilli and other Gram-positive bacteria with low GC content is the catabolite control protein A (CcpA) (4 -10). CcpA binds to catabolite responsive elements (cre) to mediate its effect (11,12). Approximately 10% of the Bacillus subtilis genome is under regulation by CcpA, underscoring its vital metabolic role (13).CcpA is a member of the LacI-GalR family of transcription regulators (14). LacI-GalR proteins contain a 60-residue N-terminal DNA binding domain that connects to a larger C-terminal domain. The C-terminal domain consists of N-and C-subdomains connected by a hinge region. (6, 24 -26). The recent structure of the CcpA-(HPr-Ser 46 -P)-cre revealed the mechanism by which HPr-Ser 46 -P functions as a corepressor for CcpA (27). Strikingly, this DNA binding activation mechanism is different from those of PurR and LacI in that CcpA utilizes a two-component phosphoprotein that is induced and stabilized by closure of its N-and C-subdomains. This mechanism involves both a rotation of CcpA subdomains as well as a relocation of the key residue Thr 61 , which is located at the interface of the DNAbinding and corepressor-binding domains. The repositioning of this residue leads to a juxtaposition of the DNA-binding domains to permit hinge helix formation in the presence of cognate DNA (15, 16).In addition to HPr, a structural and functional homologue, Crh (for catabolite repression HPr) has been identified, but only in bacilli (28). Crh...