2.A.46 The Benzoate:H Symporter (BenE) Family The BenE family contains several functionally characterized and sequenced members. Two of these are the benzoate permeases of Acinetobacter calcoaceticus (Acinetobacter baylyi) and E. coli. These proteins are about 400 residues in length and possibly span the membrane 12 times. They exhibit about 30% identity to each other and limited sequence similarity to members of the aromatic acid:H⁺ symporter (AAHS) family (2.A.1.15) of the major facilitator superfamily (MFS). However the degree of similarity with the latter proteins is insufficient to establish homology. However, the BenE family has been shown to be a member of the APC superfamily. BenE is a Na⁺ symporter (). The ortholog in Pseudomonas putida (Arthrobacter siderocapsulatus) has also been shown to be a benzoate transporter (Choudhary et al. 2017). The purine transporter, PurT_Cp of Colwellia psychrerythraea, forms a homodimer, and each protomer has 14 TMSs folded into a transport domain (core domain) and a scaffold domain (gate domain) (Weng et al. 2023). A purine base is present in the structure and defines the location of the substrate binding site. Functional studies reveal that PurT_Cp transports purines but not pyrimidines and that purine binding and transport is dependent on the pH. Mutation of a conserved aspartate residue close to the substrate binding site reveals the critical role of this residue in H⁺-dependent transport of purines. Comparison of the PurT_Cp structure with transporters of the same structural fold suggests that rigid-body motions of the substrate-binding domain are central for substrate translocation across the membrane (Weng et al. 2023). The generalized transport reactions catalyzed by membres of the BenE family are: Benzoate (out) + Na⁺ (out) → benzoate (in) + Na⁺ (in) purine (out) + H⁺ (out) → purine (in) + H⁺(in)
This family belongs to the APC Superfamily.
References:
Choudhary, A., H. Purohit, and P.S. Phale. (2017). Benzoate transport in Pseudomonas putida CSV86. FEMS Microbiol. Lett. 364:.
Neidle, E.L., C. Hartnett, L.N. Ornston, A. Bairoch, M. Rekik, and S. Harayama. (1991). Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases. J. Bacteriol. 173: 5385-5395.
Weng, J., X. Zhou, P. Wiriyasermkul, Z. Ren, K. Chen, E. Gil-Iturbe, M. Zhou, and M. Quick. (2023). Insight into the mechanism of H-coupled nucleobase transport. Proc. Natl. Acad. Sci. USA 120: e2302799120.
Examples:
TC#	Name	Organismal Type	Example
2.A.46.1.1	*Benzoate permease, BenE of 394 aas and 11 - 13 TMSs (Neidle et al.* 1991).**	Gram-negative bacteria	BenE of Acinetobacter calcoaceticus

2.A.46.1.10	*Benzoate uptake porter of 423 aas and 12 TMSs, BenE (Choudhary et al.* 2017).**		BenE of Pseudomonas putida

2.A.46.1.11	Membrane protein PurT of 471 aas and 14 TMSs. In mammals, the concentrative uptake of ascorbic acid (vitamin C) by members of the NAT family is driven by the Na⁺ gradient, while the uptake of nucleobases in bacteria is powered by the H⁺ gradient. The structure of PurC has been determined at 2.80 Å resolution (Weng et al. 2023). PurT_Cp forms a homodimer, and each protomer has 14 transmembrane segments folded into a transport domain (core domain) and a scaffold domain (gate domain). A purine base is present in the structure and defines the location of the substrate binding site. Functional studies reveal that PurT_Cp transports purines but not pyrimidines and that purine binding and transport is dependent on the pH. Mutation of a conserved aspartate residue close to the substrate binding site reveals the critical role of this residue in H⁺-dependent transport of purines. Comparison of the PurT_Cp structure with transporters of the same structural fold suggests that rigid-body motions of the substrate-binding domain are central for substrate translocation across the membrane (Weng et al. 2023).		PurT of Colwellia psychrerythraea

2.A.46.1.2	BenE homologue of 422 aas.	Actinobacteria	BenE of Rodococcus jostii

2.A.46.1.3	BenE homologue of 393 aas and 12 TMSs.	Actinobacteria	BenE of Kineococcus radiotolerans

2.A.46.1.4	BenE homologue of 398 aas and 14 TMSs.	Actinobacteria	BenE of Cellvibrio gilvus

2.A.46.1.5	BenE homologue of 398 aas and 14 TMSs	Proteobacteria	BenE of Pseudomonas putida

2.A.46.1.6	BenE homologue of 516 aas with 7 - 9 TMSs and a long hydrophiliic N-terminal domain.	Actinobacteria	BenE of Frankia sp. Ccl3

2.A.46.1.7	BenE homologue of 410 aas and 13 - 14 TMSs.	Proteobacteria	BenE of Marinobacter adhaerens

2.A.46.1.8	BenE homologue of 458 aas	Proteobacteria	BenE of Marinobacter hydrocarbonclasticus

2.A.46.1.9	YdcO (BenE homologue) of 391 aas and 13 putative TMSs.		YdcO of E. coli