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.[2] These systems have been characterized only from bacteria.
The generalized reaction for the NaT-DC family is:
R - CO− 2 (in) + H+ (out) and 1 or 2 Na+ (in) ←→ R-H + CO2 (in) and 1 or 2 Na+ (out).
Glutaconyl-CoA decarboxylase (EC 4.1.1.70; TC# 3.B.1.1.3) consists of four subunits: α (GcdA, 587 amino acyl residues (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). The catalytic subunit of all four enzyme porters are biotin-containing multi-subunit 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 Å resolution shows a dimer of TIM barrels with an active site metal ion, identified spectroscopically as Zn2+.[3]
Structure
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 (3GF3).[4] 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.[4][5]
The β-subunits possess 9 transmembrane α-helical spanners (TMSs). 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).[1][4]
Pyruvate carboxylase (PC) encoded by the gene PC is an enzyme of the ligase class that catalyzes the physiologically irreversible carboxylation of pyruvate to form oxaloacetate (OAA).
Carboxy-lyases, also known as decarboxylases, are carbon–carbon lyases that add or remove a carboxyl group from organic compounds. These enzymes catalyze the decarboxylation of amino acids, beta-keto acids and alpha-keto acids.
Oxaloacetate decarboxylase is a carboxy-lyase involved in the conversion of oxaloacetate into pyruvate.
Oxidative decarboxylation is a decarboxylation reaction caused by oxidation. Most are accompanied by α- Ketoglutarate α- Decarboxylation caused by dehydrogenation of hydroxyl carboxylic acids such as carbonyl carboxylic acid, malic acid, isocitric acid, etc.
Propionyl-CoA carboxylase (EC 6.4.1.3, PCC) catalyses the carboxylation reaction of propionyl-CoA in the mitochondrial matrix. PCC has been classified both as a ligase and a lyase. The enzyme is biotin-dependent. The product of the reaction is (S)-methylmalonyl CoA.
Carboxylation is a chemical reaction in which a carboxylic acid is produced by treating a substrate with carbon dioxide. The opposite reaction is decarboxylation. In chemistry, the term carbonation is sometimes used synonymously with carboxylation, especially when applied to the reaction of carbanionic reagents with CO2. More generally, carbonation usually describes the production of carbonates.
In enzymology, a methylmalonyl-CoA carboxytransferase is an enzyme that catalyzes the chemical reaction
In enzymology, a glutaconyl-CoA decarboxylase (EC 4.1.1.70) is an enzyme that catalyzes the chemical reaction
In enzymology, a methylmalonyl-CoA decarboxylase (EC 7.2.4.3) is an enzyme that catalyzes the chemical reaction
In enzymology, a biotin carboxylase (EC 6.3.4.14) is an enzyme that catalyzes the chemical reaction
Malonyl-S-ACP:biotin-protein carboxyltransferase is an enzyme with systematic name malonyl-(acyl-carrier protein):biotinyl-(protein) carboxytransferase. This enzyme catalyses the following chemical reaction
Acetyl-S-ACP:malonate ACP transferase is an enzyme with systematic name acetyl-(acyl-carrier-protein):malonate S-(acyl-carrier-protein)transferase. This enzyme catalyses the following chemical reaction
Malonyl-S-ACP decarboxylase (EC 4.1.1.87, malonyl-S-acyl-carrier protein decarboxylase, MdcD/MdcE, MdcD,E) is an enzyme with systematic name malonyl-(acyl-carrier-protein) carboxy-lyase. This enzyme catalyses the following chemical reaction
Biotin-independent malonate decarboxylase (EC 4.1.1.88, malonate decarboxylase (without biotin), malonate decarboxylase, MDC) is an enzyme with systematic name malonate carboxy-lyase (biotin-independent). This enzyme catalyses the following chemical reaction
Biotin-dependent malonate decarboxylase (EC 4.1.1.89, malonate decarboxylase (with biotin), malonate decarboxylase) is an enzyme with systematic name malonate carboxy-lyase (biotin-dependent). This enzyme catalyses the following chemical reaction
Carboxybiotin decarboxylase (EC 7.2.4.1, MadB, carboxybiotin protein decarboxylase) is an enzyme with systematic name carboxybiotinyl-(protein) carboxy-lyase. This enzyme catalyses the following chemical reaction
Acetate—[acyl-carrier protein] ligase is an enzyme with systematic name acetate:(acyl-carrier-protein) ligase (AMP-forming). This enzyme catalyses the following chemical reaction
Propionigenium modestum is a species of gram-negative, strictly anaerobic bacteria. It is rod-shaped and around 0.5-0.6 x 0.5-2.0μm in size. It is important in the elucidation of mechanism of ATP synthase.
Yoshito Kaziro was a Japanese biochemical and medical scientist who performed research on the effects and mechanisms of ATP and GTP driven conformational changes in enzymes and intracellular signaling pathways for over 50 years. He is well-known for his research on various signal transduction pathways involving GTP-binding proteins and the mechanism for biotin dependent carboxylation reactions of Coenzyme A (CoA) proteins.
↑ Boiangiu CD, Jayamani E, Brügel D, Herrmann G, Kim J, Forzi L, Hedderich R, Vgenopoulou I, Pierik AJ, Steuber J, Buckel W (1 January 2005). "Sodium ion pumps and hydrogen production in glutamate fermenting anaerobic bacteria". Journal of Molecular Microbiology and Biotechnology. 10 (2–4): 105–19. doi:10.1159/000091558. PMID16645308. S2CID22898166.
↑ Braune A, Bendrat K, Rospert S, Buckel W (January 1999). "The sodium ion translocating glutaconyl-CoA decarboxylase from Acidaminococcus fermentans: cloning and function of the genes forming a second operon". Molecular Microbiology. 31 (2): 473–87. doi:10.1046/j.1365-2958.1999.01189.x. PMID10027965. S2CID35018668.
Buckel W (May 2001). "Sodium ion-translocating decarboxylases". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1505 (1): 15–27. doi:10.1016/s0005-2728(00)00273-5. PMID11248185.
Cohen GN, Barbe V, Flament D, Galperin M, Heilig R, Lecompte O, Poch O, Prieur D, Quérellou J, Ripp R, Thierry JC, Van der Oost J, Weissenbach J, Zivanovic Y, Forterre P (March 2003). "An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi". Molecular Microbiology. 47 (6): 1495–512. doi:10.1046/j.1365-2958.2003.03381.x. PMID12622808. S2CID28940586.
Dimroth P (January 1997). "Primary sodium ion translocating enzymes". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1318 (1–2): 11–51. doi:10.1016/s0005-2728(96)00127-2. PMID9030254.
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