User:Jennifer VanAusdall/Sandbox 1
From Proteopedia
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==APC Superfamily== | ==APC Superfamily== | ||
| - | The amino acid/polyamine/organocation (APC) superfamily is among the largest transport superfamilies identified. | + | 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 only one has been successfully analyzed by x-ray chromatography. This one structure lends much insight into the qualities of the superfamily as a whole when compared with existing hydropathy plots and other 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 structure of AdiC, a member of the APC superfamily discussed below, is 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). | |
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| + | 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 (source). 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== | ==10 established protein families== | ||
Revision as of 19:02, 3 October 2010
Contents |
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 only one has been successfully analyzed by x-ray chromatography. This one structure lends much insight into the qualities of the superfamily as a whole when compared with existing hydropathy plots and other 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 structure of AdiC, a member of the APC superfamily discussed below, is 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).
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 (source). 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.
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.
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.
LAT1 - an example from the LAT family
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 E. coli and other bacteria. Agmatine is the product of arginine decarboxylation. By exchanging intracellular agmatine (Agm(2+)) for extracellular arginine (Arg(+)), AdiC removes protons from the interior of the cell, enabling the bacteria to survive in acidic conditions.
Though the structure is shown as a homodimer, each subunit is an independently functioning transporter. (source)
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Trp-293 has been demonstrated to be vital for substrate recognition (Casagrande). Trp-293 is buried in the substrate-binding site, Notice the aromatic interactions with the substrate.
