The AzgA purine/H(+) symporter of Aspergillus nidulans is the founding member of 
a functionally and phylogenetically distinct transporter family present in 
fungi, bacteria and plants. Here a valid AzgA topological model is built based 
on the crystal structure of the Escherichia coli uracil transporter UraA, a 
member of the nucleobase-ascorbate transporter (NAT/NCS2) family. The model 
consists of 14 transmembrane, mostly α-helical, segments (TMSs) and cytoplasmic 
N- and C-tails. A distinct compact core of 8 TMSs, made of two intertwined 
inverted repeats (TMSs 1-4 and 8-11), is topologically distinct from a flexible 
domain (TMSs 5-7 and 12-14). A putative substrate binding cavity is visible 
between the core and the gate domains. Substrate docking, molecular dynamics and 
mutational analysis identified several residues critical for purine binding 
and/or transport in TMS3, TMS8 and TMS10. Among these, Asn131 (TMS3), Asp339 
(TMS8) and Glu394 (TMS10) are proposed to directly interact with substrates, 
while Asp342 (TMS8) might be involved in subsequent substrate translocation, 
through H(+) binding and symport. Thus, AzgA and other NAT transporters use 
topologically similar TMSs and amino acid residues for substrate binding and 
transport, which in turn implies that AzgA-like proteins constitute a distant 
subgroup of the ubiquitous NAT family.