TCDB is operated by the Saier Lab Bioinformatics Group
TCIDNameDomainKingdom/PhylumProtein(s)
*3.B.1.1.1









Na+-transporting oxalo-acetate decarboxylase. Subunit stoichiometries have been described (Balsera et al., 2011). 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).

Bacteria
Proteobacteria
Oxaloacetate decarboxylase of Salmonella typhimurium
*3.B.1.1.2









Na+-transporting methylmalonyl-CoA decarboxylase
Bacteria
Firmicutes
Methylmalonyl-CoA decarboxylase of Veillonella parvula
*3.B.1.1.3









Na+-transporting glutaconyl-CoA decarboxylase
Bacteria
Firmicutes
Glutaconyl-CoA decarboxylase of Acidaminococcus fermentans
*3.B.1.1.4









Na+-transporting malonate decarboxylase
Bacteria
Proteobacteria
Malonate decarboxylase of Malonomonas rubra
*3.B.1.1.5









Putative Na+-transporting methylmalonyl-CoA decarboxylase (Cohen et al., 2003)
Archaea
Euryarchaeota
Putative methylmalonyl-CoA decarboxylase of Pyrococcus abyssi (α,β,γ,δ subunits)
α (MmdA)
β (MmdB)
γ (MmdC)
δ (MmdD)
*3.B.1.1.6









Na+-exporting oxaloacetate decarboxylase with three subunits, OadA (α), OadB (β) and OadG (γ) of 599 aas and 0 TMSs, 433 aas and 11 TMSs, and 90 aas and 1 TMS, respectively.  These three subunits are 72%, 70% and 40% identical to 3.B.1.1.1.  The stoichiometry of the three subunits is 4:2:2, and large amounts of the protein can be generated for crystalographic studies (Inoue and Li 2015).

Bacteria
Proteobacteria
OadABG of Vibrio cholerae
*3.B.1.1.7









Na+-pumping glutaconyl-CoA decarboxylase, Gcd, with subunits A4/B2/C11/C21/D2 (The stoichiometry of the subunits is given by the subscripts.). Gcd drives the endergonic translocation of Na+ across the membrane with the exergonic decarboxylation of glutaconyl-CoA (ΔG0’ ≈−30 kJ/mol) to crotonyl-CoA. Vitt et al. 2020 reported on the molecular characterization of Gcd from Clostridium symbiosum. The subunit composition is four GcdA (65 kDa), two GcdB (35 kDa), one GcdC1 (15 kDa), one GcdC2 (14 kDa), and two GcdD (10 kDa). Low-resolution structural information was achieved by electron microscopic (EM) measurements, which resulted in a 3D reconstruction model based on negative-stained particles. The Gcd structure is built up of a membrane-spanning base primarily composed of the GcdB dimer and a solvent-exposed head with the GcdA tetramer as the major component. These two globular parts are bridged by a linker presumably built up of segments of GcdC1, GcdC2 and the 2 GcdDs. The structure of the highly mobile Gcd complex represents a template for the global architecture of the Bdc family (Vitt et al. 2020).

Bacteria
Firmicutes
Glutaconyl-CoA decarboxylase, GcdABC1C2D of Clostridium symbiosum (previously mistakenly referred to as Bacteroides symbiosus)
GcdA, 558 aas
GcdB, 278 aas and 9 TMSs
GcdC1, 149 aas and 0 - 2 TMSs
GcdC2, 139 aas and 0 - 2 TMSs
GcdD, 95 aas and 1 (or maybe 2) TMSs