TCDB is operated by the Saier Lab Bioinformatics Group

3.B.1 The Na+-transporting Carboxylic Acid Decarboxylase (NaT-DC) Family

Porters of the NaT-DC family catalyze decarboxylation of a substrate carboxylic acid and use the energy released to drive extrusion of one or two sodium ions (Na+) from the cytoplasm of the cell (Boiangiu et al., 2005). These systems have been characterized only from bacteria. Distinct enzymes catalyze decarboxylation of (1) oxaloacetate, (2) methylmalonyl-CoA, (3) glutaconyl-CoA and (4) malonate. The oxaloacetate decarboxylases (EC, methylmalonyl CoA decarboxylases (EC and malonate decarboxylases are homologous. Glutaconyl-CoA decarboxylase (EC consists of four subunits: α (GcdA, 587 aas; catalytic subunit), β (GcdB, 375 aas; 9 TMSs; Na+-transporter subunit), γ (GcdC, 145 aas; biotin-carrier subunit) and δ (GcdD, 107 aas; 1 TMS; the GcdA anchor protein).

All four enzyme porters are biotin-containing multisubunit enzymes. The α-δ subunits of these enzymes are homologous to proteins encoded within the genomes of archaea, such as Pyrococcus abyssi (Cohen et al., 2003). Consequently, NaT-DC family members may be present in archaea as well as bacteria.

The α-subunits of the oxaloacetate and methylmalonyl-CoA decarboxylases are homologous to many biotin-containing enzymes including (1) pyruvate carboxylases, (2) homocitrate synthases, (3) biotin carboxyl carrier proteins, (4) isopropylmalate synthases and (5) acyl-CoA carboxylase. The α-subunit of the glutaconate decarboxylase is homologous to propionyl-CoA carboxylase.  The crystal structure of the carboxyltransferase at 1.7 A resolution shows a dimer of alpha(8)beta(8) barrels with an active site metal ion, identified spectroscopically as Zn2+ (Granjon et al. 2010).

The high resolution crystal structure of the α-subunit of the glutaconyl CoA decarboxylase (Gcdα) of Acidaminococcus fermentans (TC #3.B.1.1.3) has been solved (Wendt et al., 2003). The active site of the dimeric enzyme lies at the interface between the two monomers. The N-terminal domain binds the glutaconyl-CoA, and the C-terminal domain binds the biotinyl lysine moiety. The enzyme transfers CO2 from glutaconyl-CoA to a biotin carrier protein (the γ-subunit) that is subsequently decarboxylated by the carboxybiotin decarboxylation site within the Na+ pumping beta subunit (Gcdβ). A proposed structure of the holoenzyme positions the water-filled central channel of the Gcdα dimer coaxial with the ion channel in Gcdβ. The central channel is blocked by arginines which could allow Na+ passage by conformational movement or by entry through two side channels (Wendt et al., 2003).

The β-subunits possess 9 transmembrane α-helical spanners (TMSs), and the protein may dip into the membrane twice between TMSs III and IV. The most conserved regions are segments IIIa (the first membrane loop following TMS III) and TMS VIII. Conserved residues therein, D203 (IIIa), Y229 (IV) and N373, G377, S382 and R389 (VIII), provide Na+ binding sites and the translocation pathway. D203 and S382 may provide two binding sites for the two Na+ ions. D203 is absolutely essential for function and may provide the primary intramembranous Na+-binding site. The beta subunits of these transporters show sufficient sequence similarity to the Na+:H+ antiporters of the CPA2 family (TC #2.A.37) to establish homology (K. Studley and M.H. Saier, Jr., unpublished results).

The generalized reaction for the NaT-DC family is:

R - CO2- H+ (out) 1 or 2 Na+ (in) R - H CO2 1 or 2 Na+ (out)

This family belongs to the: CPA Superfamily.

References associated with 3.B.1 family:

Balsera, M., R.M. Buey, and X.D. Li. (2011). Quaternary structure of the oxaloacetate decarboxylase membrane complex and mechanistic relationships to pyruvate carboxylases. J. Biol. Chem. 286: 9457-9467. 21209096
Berg, M., H. Hilbi, and P. Dimroth. (1997). Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245: 103-105. 9128730
Boiangiu, C.D., E. Jayamani, D. Brugel, G. Herrmann, J. Kim, L. Forzi, R. Hedderich, I. Vgenopoulou, A.J. Pierik, J. Steuber, and W. Buckel. (2005). Sodium ion pumps and hydrogen production in glutamate fermenting anaerobic bacteria. J. Mol. Microbiol. Biotechnol. 10: 105-119. 16645308
Braune, A., K. Bendrat, S. Rospert, and W. Buckel. (1999). The sodium ion translocating glutaconyl-CoA decarboxylase from Acidaminococcus fermentans: cloning and function of the genes forming a second operon. Mol. Microbiol. 31: 473-487. 10027965
Buckel, W. (2001). Sodium ion-translocating decarboxylases. Biochim. Biophys. Acta 1505: 15-27. 11248185
Cohen, G.N., V. Barbe, D. Flament, M. Galperin, R. Heilig, O. Lecompte, O. Poch, D. Prieur, J. Quérellou, R. Ripp, J.-C. Thierry, J. Van der Oost, J. Weissenbach, Y. Zivanovic, and P. Forterre. (2003). An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol. Microbiol. 47: 1495-1512. 12622808
Di Bernardino, M. and P. Dimroth. (1996). Aspartate 203 of the oxaloacetate decarboxylase β-subunit catalyses both the chemical and vectorial reaction of the Na+ pump. EMBO J. 15: 1842-1849.
Dimroth, P. (1997). Primary sodium ion translocating enzymes. Biochim. Biophys. Acta 1318: 11-51. 9030254
Dimroth, P. and B. Schink. (1998). Energy conservation in the decarboxylation of dicarboxylic acids by fermenting bacteria. Arch. Microbiol. 170: 69-77. 9683642
Dimroth, P., P. Jockel, and M. Schmid. (2001). Coupling mechanism of the oxaloacetate decarboxylase Na+ pump. Biochim. Biophys. Acta 1505: 1-14. 11248184
Granjon, T., O. Maniti, Y. Auchli, P. Dahinden, R. Buchet, O. Marcillat, and P. Dimroth. (2010). Structure-function relations in oxaloacetate decarboxylase complex. Fluorescence and infrared approaches to monitor oxomalonate and Na+ binding effect. PLoS One 5: e10935. 20543879
Huder, J.B. and P. Dimroth. (1993). Sequence of the sodium ion pump methylmalonyl-CoA decarboxylase from Veillonella parvula. J. Biol. Chem. 268: 24564-24571. 8227015
Huder, J.B. and P. Dimroth. (1995). Expression of the sodium ion pump methylmalonyl-coenzyme A-decarboxylase from Veillonella parvula and of mutated enzyme specimens in Escherichia coli. J. Bacteriol. 177: 3623-3630. 7601825
Inoue, M. and X. Li. (2015). Highly active and stable oxaloacetate decarboxylase Na⁺ pump complex for structural analysis. Protein Expr Purif 115: 34-38. 25986323
Jockel, P., M. Di Bernardino, and P. Dimroth. (1999). Membrane topology of the β-subunit of the oxaloacetate decarboxylase Na+ pump from Klebsiella pneumoniae. Biochemistry 38: 13461-13472. 10521253
Schaffitzel, C., M. Berg, P. Dimroth, and K.M. Pos. (1998). Identification of an Na+-dependent malonate transporter of Malonomonas rubra and its dependence on two separate genes. J. Bacteriol. 180: 2689-2693. 9573154
Vitt, S., S. Prinz, N. Hellwig, N. Morgner, U. Ermler, and W. Buckel. (2020). Molecular and Low-Resolution Structural Characterization of the Na-Translocating Glutaconyl-CoA Decarboxylase From. Front Microbiol 11: 480. 32300335
Wendt, K.S., I. Schall, R. Huber, W. Buckel, and U. Jacob. (2003). Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase. EMBO J. 22: 3493-3502. 12853465
Woehlke, G., K. Wifling, and P. Dimroth. (1992). Sequence of the sodium ion pump oxaloacatate decarboxylase from Salmonella typhimurium. J. Biol. Chem. 267: 22798-22803. 1331067