The Structure of a Cyanobacterial Bicarbonate Transport Protein, CmpA

Abstract

Cyanobacteria, blue-green algae, are the most abundant autotrophs in aquatic environments and form the base of the food chain by fixing carbon and nitrogen into cellular biomass. To compensate for the low selectivity of Rubisco for CO 2 over O 2 , cyanobacteria have developed highly efficient CO 2 -concentrating machinery of which the ABC transport system CmpABCD from Synechocystis PCC 6803 is one component. Here, we have described the structure of the bicarbonatebinding protein CmpA in the absence and presence of bicarbonate and carbonic acid. CmpA is highly homologous to the nitrate transport protein NrtA. CmpA binds carbonic acid at the entrance to the ligand-binding pocket, whereas bicarbonate binds in nearly an identical location compared with nitrate binding to NrtA. Unexpectedly, bicarbonate binding is accompanied by a metal ion, identified as Ca 2؉ via inductively coupled plasma optical emission spectrometry. The binding of bicarbonate and metal appears to be highly cooperative and suggests that CmpA may co-transport bicarbonate and calcium or that calcium acts a cofactor in bicarbonate transport.Cyanobacteria are the most abundant microorganisms in aquatic environments and play a key role in the global carbon cycle (1). It is estimated that these photosynthetic microbes are responsible for ϳ50% of carbon fixation in the oceans. Over their 2.7-billion-year existence, cyanobacteria had to adapt to a changing gaseous environment where the levels of CO 2 declined and O 2 increased (2). Because O 2 can compete with CO 2 for binding to the carbon-fixing enzyme Rubisco (3), cyanobacteria evolved the most effective CO 2 -concentrating mechanism (CCM) 2 that allows them to concentrate CO 2 levels around Rubisco up to 1000-fold. The CCM involves the import and accumulation of inorganic carbon as HCO 3 Ϫ in the cytoplasm and subsequent conversion to CO 2 in the protein microcompartment called the "carboxysome" via carbonic anhydrase.One component of this CCM machinery in Synechocystis PCC 6803 is the cmpABCD operon that encodes a high affinity bicarbonate ABC transporter that is induced under low CO 2 conditions (4). This transporter is composed of four polypeptides, a high affinity solute-binding lipoprotein (CmpA), an integral membrane permease (CmpB), a cytoplasmic ATPase (CmpD), and an ATPase/solute-binding fusion protein (CmpC) that regulates transport (Fig. 1). The CmpABCD transporter is the highest affinity bicarbonate transporter of cyanobacteria (4). This affinity is predominantly conferred by the binding of bicarbonate to CmpA (K d ϭ 5 M) (5). CmpA is anchored to the periplasmic face of the cytoplasmic membrane via a lipid anchor attached to a conserved cysteine (6). The closest known homologue of CmpA is NrtA, the solute-binding protein of the nitrate-specific NrtABCD transporter that is 48% identical and 61% similar in amino acid sequence (7). We recently published an analysis (8) of the 1.6-Å structure of NrtA complexed with nitrate to elucidate the molecular determinants of nitrate specificity. From ...

The periplasmic binding protein NrtT affects xantham gum production and pathogenesis in Xanthomonas citri

“…A search of protein structures related to the NrtT amino acid sequence in the PDB corroborated the previous results, revealing five structures of the following periplasmic binding proteins: nitrate‐binding protein NrtA and carbonate‐binding protein CmpA from Synechocystis PCC 6803 22, 33, and alkanesulfonate‐binding protein SsuA from E. coli 34 and X. citri 14, which shared up to 16% amino acid sequence identity. According to the structural alignment, all the proteins conserve the secondary structures but NrtT is closely related to the structures of alkanesulfonate‐binding proteins from Methylobacillus flagelatus (PDB 3UIF), E. coli (PDB 2X26) and X. citri (PDB 3E4R) 14 (Fig.…”

Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective

“…The other two oxygen atoms are more weakly hydrogen bonded, with one in a markedly hydrophobic cleft, thereby enabling the protein to also host the nitrite anion. The system is highly homologous with a cyanobacterial bicarbonate binding protein, CmpA, which may also relate to its asymmetric coordination mode 66. Another nitrate receptor was discovered as part of the nitrate regulatory element (Nre) of staphylococci, which enables the bacteria to reduce the oxoanion instead of oxygen during anaerobic respiration.…”

In situ dynamics of O2, pH and cyanobacterial transcripts associated with CCM, photosynthesis and detoxification of ROS

“…Cyanobacteria possess a number of different genes that are induced during Ci deprivation, which allow cells to acquire and fix Ci more efficiently (Volokita et al, 1984;Badger and Price, 1990;Omata et al, 1999;Shibata et al, 2001;Maeda et al, 2002;Price et al, 2004;Zhang et al, 2004;Koropatkin et al, 2007;Folea et al, 2008;Xu et al, 2008); these low Ci-induced genes encode polypeptides that are considered as components of the CCM (Kaplan et al, 2008). The majority of ribulose-1,5-bisphosphate carboxylase in cyanobacteria is localized to a specialized microcompartment, the carboxysome, and the structural and catalytic components of the carboxysome are also considered as part of the CCM (Price et al, 2008).…”