2.A.56 The Tripartite ATP-independent Periplasmic Transporter (TRAP-T) Family

TRAP-T family permeases generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-positive bacteria and archaea. Several members of the family have been both sequenced and functionally characterized. The first system to be characterized was the DctPQM system of Rhodobacter capsulatus (Forward et al., 1997), and it is the prototype for the TRAP-T family (Kelly and Thomas, 2001; Rabus et al., 1999).  TRAPs exhibit an 'elevator-with-an-operator' mechanism (Davies et al. 2023). TRAP systems couple a substrate-binding protein (SBP) to an elevator-type secondary transporter, which is a first-of-its-kind mechanism of transport (Davies et al. 2023). TRAP transporter structures and recent functional data probe the mechanism of transport. Recent structural and biophysical studies of the ion transporter superfamily (ITS) members highlight mechanistic principles that are relevant for further exploration of the TRAP transporter system.

DctP is a periplasmic dicarboxylate (malate, fumarate, succinate) binding receptor that is biochemically well-characterized. The 3-dimensional structure of a homologue, SiaTP (TC #2.A.56.1.3) has been solved (Muller et al., 2006). DctQ is an integral cytoplasmic membrane protein (25 kDa) with 4 putative transmembrane α-helical spanners (TMSs). DctM is a second integral cytoplasmic membrane protein (50 kDa) with 12 putative TMSs. These three proteins have been shown to be both necessary and sufficient for the proton motive force-dependent uptake of dicarboxylates into R. capsulatus. An involvement of ATP in transport energization was excluded.  The substrate-binding protein, SiaP, imposes directionality on an electrochemical sodium gradient-driven TRAP transporter, SiaPQM (Mulligan et al., 2009).

In several TRAP-T systems, fused Q-M-type proteins instead of two separate Q- and M-type proteins are found, while in others, Q-P-type fusion proteins are found. The operon encoding the Synechocystis system includes a protein homologous to the glutamine binding protein, and biochemical evidence has suggested that a glutamate transporter from Rhodobacter sphaeroides is a periplasmic binding protein-dependent, pmf-dependent secondary carrier (Jacobs et al., 1996). Homologous systems in Halomonas elongata and Rhodobacter spheroides take up ectoine/hydroxyectoine and taurine, respectively (Bruggemann et al., 2004; Grammann et al., 2002). The DctP dicarboxylate receptor is homologous to both the YiaO monocarboxylate receptor and the TeaA ectoine receptor. Thus, the TRAP-T family of permeases may be involved in the uptake of widely divergent compounds, mostly carboxylate derivatives (Kelly and Thomas, 2001; Thomas et al., 2006; Mulligan et al., 2007).

The crystal structure of SiaP (the receptor for SiaTP; TC #2.A.56.1.3) reveals an overall topology similar to ATP binding cassette receptors, which is not apparent from the sequence, demonstrating that primary and secondary transporters can share a common structural component (Müller et al., 2006). The structure of SiaP in the presence of the sialic acid analogue 2,3-didehydro-2-deoxy-N-acetylneuraminic acid reveals the ligand bound in a deep cavity with its carboxylate group forming a salt bridge with a highly conserved Arg residue. Sialic acid binding, which obeys simple bimolecular association kinetics, is accompanied by domain closure about a hinge region and the kinking of an α-helix hinge component. The structure provides insight into the evolution, mechanism, and substrate specificity of TRAP-transporters (Müller et al., 2006).

The solute binding receptor, DctP, has a structure comprised of two domains connected by a hinge that closes upon substrate binding, similar to those in ABC uptake porters. Substrate binding is mediated through a conserved and specific arginine/carboxylate interaction in the receptor. Mulligan et al. (2011) have reviewed the expanding repertoire of substrates and physiological roles for experimentally characterized TRAP transporters in bacteria and discuss mechanistic aspects. TRAP transporters are high-affinity, Na⁺-dependent unidirectional secondary transporters.

A subfamily of TRAP-Ts [tetratricopeptide repeat-protein associated TRAP transporters (TPATs)] has four components. Three are common to both TRAP-Ts and TPATs. TPATs are distinguished from TRAP-Ts by the presence of a protein called the 'T component'. In Treponema pallidum, this protein (TatT) is a water-soluble trimer whose protomers are each perforated by a pore. Its respective P component (TatP(T)) interacts with TatT. Co-crystal structures of two complexes showed that up to three monomers of TatP(T) can bind to the TatT trimer. A putative ligand-binding cleft of TatP(T) aligns with the pore of TatT, strongly suggesting ligand transfer between T and P(T) (Brautigam et al., 2012).

The generalized transport reaction presumed to be catalyzed by TRAP-T family permeases is:

solute (out) + nH⁺ (out) → solute (in) + nH⁺ (in)