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). 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 generalized transport reaction presumed to be catalyzed by TRAP-T family permeases is: solute (out) + nH⁺ (out) → solute (in) + nH⁺ (in).
This family belongs to the IT Superfamily.
References:
Allen, S., A. Zaleski, J.W. Johnston, B.W. Gibson, M.A. Apicella. (2005). Novel sialic acid transporter of Haemophilus influenzae. Infect. Immun. 73: 5291-5300.
Bruggemann, C., K. Denger, A.M. Cook, and J. Ruff. (2004 ). Enzymes and genes of taurine and isethionate dissimilation in Paracoccus denitrificans. Microbiology 150: 805-816.
Chae, J.C. and G.J. Zylstra. (2006). 4-Chlorobenzoate uptake in Comamonas sp. strain DJ-12 is mediated by a tripartite ATP-independent periplasmic transporter. J. Bacteriol. 188: 8407-8412.
Denger, K., T.H. Smits, and A.M. Cook. (2006). Genome-enabled analysis of the utilization of taurine as sole source of carbon or of nitrogen by Rhodobacter sphaeroides 2.4.1. Microbiology 152: 3197-3206.
Forward, J., M.C. Behrendt, N.R. Wyborn, R. Cross, and D.J. Kelly. (1997). TRAP Transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse Gram-negative bacteria. J. Bacteriol. 179: 5482-5493.
Grammann, K., A. Volke, and H.J. Kunte. (2002). New type of osmoregulated solute transporter identified in halophilic members of the Bacteria domain: TRAP transporter TeaABC mediates uptake of ectoine and hydroxyectoine in Halomonas elongata DSM 2581^T. J. Bacteriol. 184: 3078-3085.
Jacobs, M.H.J., T. van der Heide, A.J.M. Driessen, and W.N. Konings. (1996). Glutamate transport in Rhodobacter sphaeroides is mediated by a novel binding-protein dependent secondary transport system. Proc. Natl. Acad. Sci. USA 93: 12786-12790.
Johnston, J.W., N.P. Coussens, S. Allen, J.C. Houtman, K.H. Turner, A. Zaleski, S. Ramaswamy, B.W. Gibson, and M.A. Apicella. (2008). Characterization of the N-acetyl-5-neuraminic acid-binding site of the extracytoplasmic solute receptor (SiaP) of nontypeable Haemophilus influenzae strain 2019. J. Biol. Chem. 283(2): 855-865.
Kelly, D.J. and G.H. Thomas. (2001). The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea. FEMS Microbiol. Rev. 25: 405-424.
Mulligan, C., D.J. Kelly, and G.H. Thomas. (2007). Tripartite ATP-independent periplasmic (TRAP) transporters: application of a relational database (TRAPDb) for genome-wide analysis of transporter gene frequency and organization. J. Mol. Microbiol. Biotechnol. (in press).
Mulligan, C., E.R. Geertsma, E. Severi, D.J. Kelly, B. Poolman, and G.H. Thomas. (2009). The substrate-binding protein imposes directionality on an electrochemical sodium gradient-driven TRAP transporter. Proc. Natl. Acad. Sci. USA 106: 1778-1783.
Müller, A., E. Severi, C. Mulligan, A.G. Watts, D.J. Kelly, K.S. Wilsonz, A.J. Wilkinson, and G.H. Thomas. (2006). Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae. J. Biol. Chem. 281: 22212-22222.
Quintero, M.J., M.L. Montesinos, A. Herrero, and E. Flores. (2001). Identification of genes encoding amino acid permeases by inactivation of selected ORFs from the Synechocystis genomic sequence. Genome Res. 11: 2034-2040.
Rabus, R., D.L. Jack, D.J. Kelly, and M.H. Saier, Jr. (1999). TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters. Microbiology 145: 3431-3445.
Rodionov, D.A., P. Hebbeln, A. Eudes, J. ter Beek, I.A. Rodionova, G.B. Erkens, D.J. Slotboom, M.S. Gelfand, A.L. Osterman, A.D. Hanson, and T. Eitinger. (2009). A novel class of modular transporters for vitamins in prokaryotes. J. Bacteriol. 191: 42-51.
Severi, E., G. Randle, P. Kivlin, K. Whitfield, R. Young, R. Moxon, D. Kelly, D. Hood, and G.H. Thomas. (2005). Sialic acid transport in Haemophilus influenzae is essential for lipopolysaccharide sialylation and serum resistance and is dependent on a novel tripartite ATP-independent periplasmic transporter. Mol. Microbiol. 58: 1173-1185.
Thomas, G.H., T. Southworth, M.R. Leon-Kempis, A. Leech, and D.J. Kelly. (2006). Novel ligands for the extracellular solute receptors of two bacterial TRAP transporters. Microbiology 152: 187-198.
Examples:
TC#	Name	Organismal Type	Example
2.A.56.1.1	*Tripartite dicarboxylate:H⁺ symporter (substrates include: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate and mesaconate) (Forward et al., 1997)*	Gram-negative bacteria	DctPQM dicarboxylate transporter of Rhodobacter capsulatus DctP (R) DctQ (M, 4 TMS) DctM (M, 12 TMS)

2.A.56.1.2	*The 2,3-diketo-L-gulonate (2,3-DKG) transporter, YiaMNO [2,3-KDG is a breakdown product of L-ascorbate] (Thomas et al., 2006)*	Bacteria	YiaMNO of E. coli YiaM (M, 4 TMSs; most like TauL) (P37674) YiaN (M, 12 TMSs; most like DctM) (P37675) YiaO (R, like DctP and TauK) (P37676)

2.A.56.1.3	*Sialic acid (N-acetyl neuraminic acid) transporter, SiaTP (Allen et al., 2005; Severi et al., 2005; Johnston et al., 2008)*	Bacteria	SiaTP of Haemophilus influenzae SiaT (a fusion protein equivalent to both DctM and DctQ) (616 aas; 16 TMSs) (P44543) SiaP (R) (P44544)

2.A.56.1.4	*Putative tripartite taurine uptake system, TauKLM (Bruggemann et al., 2004; Denger et al., 2006)*	Bacteria	TauKLM of Rhodobacter sphaeroides TauK (Rsph2615) (R) (Q3IVI6) TauL (Rsph2614) (M, 4 TMS) (Q3IVI5) TauM (Rsph2613) (M, 12 TMS) (Q3IVI4)

2.A.56.1.5	The 2-ketomonocarboxylate transporter (presented in order of affinity - 2-oxovalerate [highest affinity, Kd=0.1 μM], 2-oxoisovalerate, 2-oxobutyrate, 2-oxoisocaproate, 2-oxo-3-methylvalerate, pyruvate [lowest affinity, Kd=3 μM]) (Thomas et al., 2006)	Bacteria	The 2-ketomonocarboxylate transporter of Rhodobacter capsulatus M-large (RRC02479) M-small (RRC02478) R (RRC01191)

2.A.56.1.6	*The putative rhamnogalacturonide transporter (Rodionov et al., 2009)*	Proteobacteria	RhiABC of Salmonella typhimurium RhiA (R) (P43020) RhiB (M, 4 TMSs) (Q8ZKR9) RhiC (M, 12 TMSs) (Q8ZKS0)

Examples:
TC#	Name	Organismal Type	Example
2.A.56.2.1	*Tripartite high affinity ectoine/hydroxyectoine uptake system (Grammann et al., 2002)*	Bacteria	TeaABC ectoine transporter of Halomonas elongata TeaA (R) TeaB (M, 4 TMS) TeaC (M, 12 TMS)

Examples:
TC#	Name	Organismal Type	Example
2.A.56.3.1	*Tripartite glutamate:Na⁺ symporter (Quintero et al., 2001)*	Gram-negative bacteria	GtrABC glutamate:Na⁺ symporter of Synechocystis strain PCC6803 GtrA (M) (like DctQ) GtrB (M) (like DctM) GtrC (R) (like GlnH of E. coli)

2.A.56.3.2	Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (Chae and Zylstra, 2006)	Gram-negative bacteria	FcbT1/T2/T3 of Comamonas sp. strain DJ-12 FcbT1 (R) (AAF16407) FcbT2 (M-sm) (AAF16408) FcbT3 (M-lg) (AAF16409)