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TopicPage for Nucleobase permeases of Escherichia coli K-12

Paralogs

Description:

The NAT (Nucleobase/Ascorbate Transporter) family includes prokaryotic purine and pyrimidine permeases mediating base uptake for recycling and for use as nitrogen sources, including 10 known and predicted E. coli nucleobase permeases. The NAT family also includes eukaryotic ascorbate transporters. The NAT family is also known as the Nucleobase:Cation Symporter-2 (NCS2) family (see TCDB 2.A.40) and is often referred to as the xanthine/uracil permease family (de Koning, 2000). The NAT family is defined by Pfam family signature PF00860 and by NCBI CD superfamily cl00967.

The NAT family is part of the large Amino acid-Polyamine-organoCation (APC) superfamily defined by Pfam clan CL0062. The NAT family contains two distinct sub-families defined by NCBI COG2233 and COG2252 clusters, with six and four E. coli K-12 members, respectively. The six COG2233 sub-family E. coli members include the xanthine permeases YicE and YgfO (Karatza, 2005) and the uracil permease UraA, as well as other characterized purine and pyrimidine permeases from all three kingdoms. The COG2252 subfamily was combined into the NAT family as a distant branch and several members were characterized as purine permeases. Bacillus subtilis has two COG2252 guanine-hypoxanthine permeases: PbuG and PbuO (Saxild, 1987;1988; 2001). Subsequently, the COG2252 hypoxanthine-adenine-guanine permease AzgA of Aspergillus nidulans was characterized (Cecchetto, 2004). The initially characterized member of the COG2252 subfamily is the E. coli PurP adenine permease (Burton, 1977; 1983; 1994). The PurP sequence was published in 1994, but was only recenly annotated in sequence databases, so its founding role has been overlooked. In contrast to COG2233, COG2252 members may be restricted to purine permeases. The six E. coli K-12 COG2233 members are referred to as the UraA subfamily and the four COG2252 members are referred to as the PurP subfamily.

Details:

Three of the COG2233 family, also known as the NAT/NCS2 transporter family, paralogs are known xanthine or uracil permeases, including UraA. And although the substrate specificity of RutG is untested, it is in an operon for pyrimidine nitrogen catabolism and is likely to be a pyrimidine permease. None of the four distantly related COG2252 permeases have being tested and the substrate specificity range of this family is unknown. YgfQ is 35 bp downstream of the guaD gene for guanine deaminase and it might be a guanine permease. YicO is adjacent to the ade gene for adenine deaminase and might be an adenine permease. Unlike the COG2233 family, the COG2252 family might be specific for purine substrates.

Family Tree

A paralogous family tree was generated from a clustalx alignment with njplot and drawn using the Phylodendron webserver. This tree illustrates the two COG families and the YbbY offshoot, as well as some close pairwise relationships.
UraA_tree