The single most important nutrient for photosynthesis and growth is nitrate, which is severely limiting in many aquatic environments such as the open ocean.  Therefore, the cyanobacteria have developed a high-affinity ABC transport system that is composed of four polypeptides (Figure 1): a high-affinity periplasmic solute-binding lipoprotein (NrtA), an integral membrane permease (NrtB), a cytoplasmic ATPase (NrtD), and a unique ATPase/solute-binding fusion protein (NrtC) that regulates transport.  NrtA binds both nitrate and nitrite (Kd = 0.3 mM) and is necessary for cell survival when nitrate is the primary nitrogen source. The role of NrtA is to scavenge nitrate/nitrite from the periplasm for delivery to the membrane permease, NrtB.  The passage of solute through the transmembrane pore is linked to ATP hydrolysis by NrtC and NrtD.  NrtD consists of a single ATPase domain.  In contrast, NrtC contains both an ATPase domain and a C-terminal solute-binding domain that shares 50% amino acid sequence similarity with NrtA, and is required for the ammonium-mediated inhibition of nitrate transport.  Aside from the homologous transporter for bicarbonate, CmpABCD, there are no other known examples of ABC transporters that have an ATPase/solute-binding fusion component. Here we describe the first structure of a nitrate-specific receptor, NrtA from Synechocystis sp. PCC 6803, complexed with nitrate and determined to a resolution of 1.5Å.  NrtA is significantly larger than other oxyanion-binding proteins, representing a new class of transport proteins.  From sequence alignments, the only other solute-binding protein in this class is CmpA, a bicarbonate-binding protein.  Therefore, these organisms created a novel solute-binding protein for two of the most important nutrients; inorganic nitrogen and carbon.  The electrostatic charge distribution of NrtA appears to force the protein off the membrane while the flexible tether facilitates the delivery of nitrate to the membrane pore.  The structure not only details the determinants for nitrate selectivity in NrtA, but also the bicarbonate specificity in CmpA.  Nitrate and bicarbonate transport are regulated by the cytoplasmic proteins NrtC and CmpC, respectively.  Interestingly, the residues lining the ligand binding pockets suggest that they both bind nitrate.  This implies that the nitrogen and carbon uptake pathways are synchronized by intracellular nitrate and nitrite.
Cartoon representation of the assembled NrtABCD nitrate transporter. NrtA is tethered to the periplasmic membrane by a flexible linker and captures nitrate/nitrite in the periplasm for delivery to the transmembrane complex created by NrtB.  In many ABC transporters, the transmembrane pore is created by a dimer of two transmembrane spanning polypeptides. NrtC and NrtD are ATPases which couple ATP hydrolysis to nitrate/nitrite transport through the pore.  NrtC is unique in that it contains a C-terminal solute-binding domain homologous to NrtA.
	The structure of NrtA.  Left: Ribbon representation of the NrtA crystal structure colored blue to red as the chain extends from the N-terminus to the C-terminus.  NrtA consists of two α/β domains arranged with a C-clamp shape, with nitrate, depicted as spheres, bound in the cleft between the two domains. The view is of the front of the C-clamp, which opens to the nitrate-binding cleft. Right: Electrostatic surface potential of the back of the NrtA structure, with positive and negative charge shown in blue and red, respectively.  This charge on the back of the NrtA is likely to keep it off the cell membrane and thereby making it interact more efficiently with the transmembrane pore.
Schematic representation of the nitrate-binding site.  Shown here are the protein-ligand interactions between NrtA and nitrate with all potential hydrogen-bonding and electrostatic interactions depicted as dashed lines.
Model for synergistic regulation of nitrate and bicarbonate uptake.  From structure and sequence analysis, it is clear that NrtA is highly homologous to the regulatory protein for the bicarboante transport system.  Therefore, we propose that nitrate may regulate both bicarbonate and nitrate uptake.  As shown in this model, both the Nrt (cyan) and Cmp (green) complexes are inhibited by nitrate (yellow balls).  If energy or nutrient supplies were to become limiting, both nitrogen and carbon fixation is blocked and the levels of ammonium (mauve balls) would rise.  This, in turn, increases the concentration of nitrate and shut down both bicarbonate and nitrate uptake.  It is logical to have nitrate act as the feedback regulator since its reduction to membrane permeable ammonia (dark blue balls) would waste a great deal of cellular reductive potential if not fully utilized by carbon and nitrogen fixation pathways.

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