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APC Superfamily

The amino acid/polyamine/organocation (APC) superfamily is among the largest transport superfamilies identified. It is found in all forms of life. However, not much is known about the structures of members of this family, because not many proteins have been crystallized. These few structures lend much insight into the qualities of the superfamily as a whole when compared with existing hydropathy plots and other structural studies.

Superfamilies have been identified using phylogenetic analysis. Thus, only proteins with similar genetic qualities and evolutionary roots are considered members of the same superfamily. Because of this, proteins with similar topographies are not necessarily in the same superfamily. For instance, the core structures of ApcT and AdiC, members of the APC superfamily discussed below, are very similar to that of LeuT (a member of the neurotransmitter sodium symporter (NSS) family), BetP (a member of the betaine/chlorine/carnitine transporter (BCCT) family), vSGLT (of the solute sodium symporter (SSS) family) and Mhb1 (of the nucleobase-cation-symport-1 (NCS1) family)[1]

According to hydropathy plots [2], all members of the APC superfamily exhibit a uniform topology formed by a single polypeptide chain that crosses the plasma membrane 12 times, unless otherwise noted. All of these proteins also share a similar structural core, consisting of two V-shaped domains of five transmembrane domains each, intertwined in an antiparallel topology. [3] Each protein's N- and C-termini are located in the cytosol. The loops in the cytosol tend to be smaller than the loops located in the extracellular space.

10 established protein families

AAT: Amino Acid Transporter

Unique to bacteria, this is the largest family within the APC superfamily. Members of this family have short hydrophilic extensions at both termini.

APA: Basic Amino Acid/Polyamine Transporter

The APA family is also unique to bacteria.

CAT: Cationic Amino Acid Transporter

Members of the CAT family are ubiquitous, containing 14 TMs in eukaryotes and 12 TMs in prokaryotes. These proteins have short, hydrophilic, N-terminal extensions. CAT2 provides arginine for NO synthesis (12) and for arginase (13) in classical and alternative activation of macrophages, and CAT1 is required for macrophage proliferation [4]

ACT: Amino Acid/Choline Transporter

Members of the CAT family can be found in yeast, plants, and fungi. These proteins have short hydrophilic extensions at the C and N termini.

EAT: Ethanolamine Transporter

Members of the EAT family are found in bacteria. They have no noticeable extensions beyond the 12 TMs.

ABT: Archaeal/Bacterial Transporter

As the name suggests, members of the ABT family are found in archaea and bacteria. One member (Cat1 Afu) of this family exhibits a long, C-terminal extension that may function in interactions with other proteins.

GGA: Glutamate:GABA Antiporter

Members of the GGA family are found only in bacteria. There proteins have short, hydrophilic, N-terminal extensions.

LAT: L-type Amino Acid Transporter

Members of the LAT family have been identified in animals and yeast.

SPG: Spore Germination Protein

Members of this family are found in prokaryotes and exhibit only 10 transmembrane segments. The 2 segments closest to the C-terminus in other members of this super family appear to have been cleaved when this family was evolving. None of the proteins in this family have been identified as transporters, leading to the possibility that transmembrane segments 11 and 12 are vital for transport function.

YAT: Yeast Amino Acid Transporter

Members of the YAT family have been identified in both yeast and fungi. Some members of this family exhibit long, N-terminal, hydrophilic extensions beyond the 12 TMs.

ApcT - a proton-coupled amino acid transporter

ApcT in high pH, inward facing, apo conformation [3GIA]

Drag the structure with the mouse to rotate
where the N-terminus is gradually shaded into the C-terminus according to the scale below.
N               C

ApcT is cylindrical in shape with 12 TM domains (numbered from N-terminus to C-terminus), short intracellular and extracellular loops, and each termini ending in the cytoplasm, consistent with the topography of AdiC described below. ApcT is a proton-coupled, broad specificity transporter. It transports a range of amino acids (l-Glu, l-Ala, > l-Ser, l-Gln >l-Phe,) but transports the smallest (Gly) or largest (Trp) amino acids very slowly, if at all [5]. Lys-158, has been proposed to be necessary for proton coupled transport in this protein.


AdiC - an example from the APA family

AdiC has been determined to be a member of the APC superfamily through phylogenetic analysis.

AdiC is a representative member of the APC superfamily; it contains 12 TMs with each termini located in the cytosol. AdiC functions as an arginine/agmatine antiporter in Escherichia coli, Salmonella enterica serovar Typhimurium[6], and other bacteria when the cell is exposed to acidic environments. Agmatine is the product of arginine decarboxylation. An associated protein, AdiA[7], is thought to decarboxylate arginine molecules for transport. By exchanging intracellular agmatine (Agm(2+)) for extracellular arginine (Arg(+)), AdiC removes virtual protons from the interior of the cell, enabling the bacteria to survive in acidic conditions by preventing acidification of the cytosol.

Outward-facing AdiC homodimer [3LRB]

Drag the structure with the mouse to rotate
Though the structure is shown as a homodimer, each subunit is an independently functioning transporter. [8]

As in ApcT, 10 of the transmembrane helices surround the pore in antiparallel fashion, with TM1 paired with TM6, TM2 with TM7, and so on. TMs 11 and 12 do not participate in this pairing scheme; instead, they form most of the homodimeric interface. TMs 1 and 6 contain short, non-helical, Gly-containing loops midway across the membrane, thought to be important for substrate interactions [9]. Amino acids in these loops are highly conserved within distinct families of the APC superfamily. For example, AdiC, CadB, and PotE, which all belong to the APA family, share two signature loop sequences, the GSG motif (Gly25-Ser26-Gly27) in TM1 and the GVESA motif (Gly206-Val-Glu-Ser-Ala210) in TM6.

AdiC in complex with Arginine and B-Nonylglucoside [3L1L]

Drag the structure with the mouse to rotate
Arg binding induces a structural rearrangement in TM6 and minor changes in TM2 and TM10, resulting in an occluded formation [10]. The occluded formation materializes upon binding of a substrate.

Trp-293 has been demonstrated to be vital for substrate recognition [11]. Trp-293 is buried in the substrate-binding site, Notice the aromatic interactions with the substrate. Tyr-93 is another residue proposed to be vital for substrate specificty and/or binding, Trp-293 and Tyr-93 come from TM8 and TM3, respectively.
Glu-208 also appears to have a role in regulating the upload and release of substrate by acting as a pH sensor. In the stomach (pH 2-3), Glu-208 (pKa approx 4.25) is likely protonated while other residues with a pKa of approx 2 are mostly unprotonated. Thus, the majority of these amino acids carry no net charge on their head groups, with the positively charged a-amino group offsetting the negatively charged a-carboxyl group. Protonated Glu-208 likely binds to the neutral head groups of the substrate amino acid (arginine). Once facing the intracellular environment (pH 4-5), Glu-208 is likely to deprotonate, developing a net negative charge in the substrate-binding cavity. The negative charge may attract positively charged head group of the a-decarboxylated amino acid (agmatine) and favor its binding. When this occurs, agmatine replaces arginine in the binding site, releasing arginine into the cytosol and initiating the deportation of the agmatine.

LAT1 and SteT - examples from the LAT family

References

  1. ↑ Lolkema JS, Slotboom DJ. The major amino acid transporter superfamily has a similar core structure as Na+-galactose and Na+-leucine transporters. Mol Membr Biol. 2008 Sep;25(6-7):567-70. Epub 2008 Nov 21. PMID:19031293 doi:10.1080/09687680802541177
  2. ↑ Jack DL, Paulsen IT, Saier MH. The amino acid/polyamine/organocation (APC) superfamily of transporters specific for amino acids, polyamines and organocations. Microbiology. 2000 Aug;146 ( Pt 8):1797-814. PMID:10931886
  3. ↑ Vangelatos I, Vlachakis D, Sophianopoulou V, Diallinas G. Modelling and mutational evidence identify the substrate binding site and functional elements in APC amino acid transporters. Mol Membr Biol. 2009 Aug;26(5):356-70. Epub 2009 Aug 7. PMID:19670073 doi:913775369
  4. ↑ x
  5. ↑ Shaffer PL, Goehring A, Shankaranarayanan A, Gouaux E. Structure and Mechanism of a Na+ Independent Amino Acid Transporter. Science. 2009 Jul 22. PMID:19608859
  6. ↑ Smith CB, Graham DE. Outer and inner membrane proteins compose an arginine-agmatine exchange system in Chlamydophila pneumoniae. J Bacteriol. 2008 Nov;190(22):7431-40. Epub 2008 Sep 12. PMID:18790867 doi:10.1128/JB.00652-08
  7. ↑ Kieboom J, Abee T. Arginine-dependent acid resistance in Salmonella enterica serovar Typhimurium. J Bacteriol. 2006 Aug;188(15):5650-3. PMID:16855258 doi:10.1128/JB.00323-06
  8. ↑ Fang Y, Jayaram H, Shane T, Kolmakova-Partensky L, Wu F, Williams C, Xiong Y, Miller C. Structure of a prokaryotic virtual proton pump at 3.2 A resolution. Nature. 2009 Aug 20;460(7258):1040-3. Epub 2009 Jul 5. PMID:19578361 doi:10.1038/nature08201
  9. ↑ Gao X, Lu F, Zhou L, Dang S, Sun L, Li X, Wang J, Shi Y. Structure and mechanism of an amino acid antiporter. Science. 2009 Jun 19;324(5934):1565-8. Epub 2009 May 28. PMID:19478139
  10. ↑ Gao X, Zhou L, Jiao X, Lu F, Yan C, Zeng X, Wang J, Shi Y. Mechanism of substrate recognition and transport by an amino acid antiporter. Nature. 2010 Feb 11;463(7282):828-32. Epub 2010 Jan 20. PMID:20090677 doi:10.1038/nature08741
  11. ↑ Fang Y, Jayaram H, Shane T, Kolmakova-Partensky L, Wu F, Williams C, Xiong Y, Miller C. Structure of a prokaryotic virtual proton pump at 3.2 A resolution. Nature. 2009 Aug 20;460(7258):1040-3. Epub 2009 Jul 5. PMID:19578361 doi:10.1038/nature08201

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