TCDB is operated by the Saier Lab Bioinformatics Group

2.A.39 The Nucleobase:Cation Symporter-1 (NCS1) Family

The NCS1 family consists of over 1000 currently sequenced proteins derived from Gram-negative and Gram-positive bacteria, archaea, yeast, fungi and plants. The bacterial and yeast proteins are widely divergent and do not cluster closely on the NCS1 family phylogenetic tree. B. subtilis possesses two paralogues of the NCS1 family, and S. cerevisiae has several. Two of the yeast proteins (Dal4 and Fur4) cluster tightly together, and three other S. cerevisiae proteins, one of which is the thiamin permease, Thi10, and another of which is the nicotinamide riboside transporter, Nrt1 (Belenky et al., 2008), also cluster tightly together. The latter three proteins are likely to be closely-related thiamin permease isoforms. The yeast cytosine-purine and vitamin B6 transporters cluster loosely together (24% identity; e-50 (Stolz and Vielreicher, 2003). The bacterial proteins are derived from several Gram-negative and Gram-positive species. These proteins exhibit limited sequence similarity with the xanthine permease, PbuX, of Bacillus subtilis which is a member of the NCS2 family. The two families are therefore probably related.

Proteins of the NCS1 family are 419-635 amino acyl residues long and possess twelve putative transmembrane α-helical spanners (TMSs). At least some of them have been shown to function in uptake by substrate:H+ symport. In these respects, and with respect to substrate specificity, these proteins resemble the symporters of the NCS2 family, providing further evidence that the two families represent distant constituents of a single superfamily. The two families probably arose by an early gene duplication event that occurred long before divergence of the three major kingdoms of life. It is possible that they are distant constituents of the MFS (2.A.1).

The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Weyand et al. 2008 reported the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport (Weyand et al. 2008).

NCS1 proteins are H+/Na+ symporters specific for the uptake of purines, pyrimidines and related metabolites. Krypotou et al. 2015 studied the origin, diversification and substrate specificities of fungal NCS1 transporters, suggesting that the two fungal NCS1 subfamilies, Fur and Fcy, and plant homologues, originated through independent horizontal transfers from prokaryotes.  Expansion by gene duplication led to functional diversification of fungal NCS1 porters. They characterized all Fur proteins in Aspergillus nidulans. Homology modelling, substrate docking, molecular dynamics and systematic mutational analysis in three Fur transporters with distinct specificities identified residues critical for function and specificity, located within a major substrate binding site, in transmembrane segments TMS1, TMS3, TMS6 and TMS8. They predicted and confirmed that residues determining substrate specificity are located not only in the major substrate binding site, but also in a putative outward-facing selectivity gate. Their evolutionary and structure-function analyses led to the concept that selective channel-like gates may contribute to substrate specificity (Krypotou et al. 2015).

The generalized transport reaction catalyzed by NCS1 family permeases is:

Nucleobase or Vitamin (out) + H+ (out) → Nucleobase or Vitamin (in) + H+ (in)

This family belongs to the: APC Superfamily.

References associated with 2.A.39 family:

Belenky, P.A., T.G. Moga, and C. Brenner. (2008). Saccharomyces cerevisiae YOR071C encodes the high affinity nicotinamide riboside transporter Nrt1. J. Biol. Chem. 283: 8075-8079. 18258590
Danielsen, S., M. Kilstrup, K. Barilla, B. Jochimsen, and J. Neuhard. (1992). Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase. Mol. Microbiol. 6: 1335-1344. 1640834
De Koning, H. and G. Diallinas. (2000). Nucleobase transporters. Molec. Memb. Biol. 75: 75-94.
Enjo, F., K. Nosaka, M. Ogata, A. Iwashima, and H. Nishimura. (1997). Isolation and characterization of a thiamin transport gene, THI10, from Saccharomyces cerevisiae. J. Biol. Chem. 272: 19165-19170. 9235906
Gabriel, F., A. Sabra, S. El-Kirat-Chatel, S. Pujol, V. Fitton-Ouhabi, D. Brèthes, K. Dementhon, I. Accoceberry, and T. Noël. (2014). Deletion of the uracil permease gene confers cross-resistance to 5-fluorouracil and azoles in Candida lusitaniae and highlights antagonistic interaction between fluorinated nucleotides and fluconazole. Antimicrob. Agents Chemother. 58: 4476-4485. 24867971
Goudela, S., H. Tsilivi, and G. Diallinas. (2006). Comparative kinetic analysis of AzgA and Fcy21p, prototypes of the two major fungal hypoxanthine-adenine-guanine transporter families. Mol. Membr. Biol. 23: 291-303. 16923723
Kazmier K., Sharma S., Islam SM., Roux B. and Mchaourab HS. (2014). Conformational cycle and ion-coupling mechanism of the Na+/hydantoin transporter Mhp1. Proc Natl Acad Sci U S A. 111(41):14752-7. 25267652
Krypotou E., Kosti V., Amillis S., Myrianthopoulos V., Mikros E. and Diallinas G. (2012). Modeling, substrate docking, and mutational analysis identify residues essential for the function and specificity of a eukaryotic purine-cytosine NCS1 transporter. J Biol Chem. 287(44):36792-803. 22969088
Krypotou, E., T. Evangelidis, J. Bobonis, A.A. Pittis, T. Gabaldón, C. Scazzocchio, E. Mikros, and G. Diallinas. (2015). Origin, diversification and substrate specificity in the family of NCS1/FUR transporters. Mol. Microbiol. 96: 927-950. 25712422
Ma, P., S.G. Patching, E. Ivanova, J.M. Baldwin, D. Sharples, S.A. Baldwin, and P.J. Henderson. (2016). The allantoin transport protein, PucI, from Bacillus subtilis: evolutionary relationships, amplified expression, activity and specificity. Microbiology. [Epub: Ahead of Print] 26967546
Moraes, T.F. and R.A. Reithmeier. (2012). Membrane transport metabolons. Biochim. Biophys. Acta. 1818: 2687-2706. 22705263
Papadaki, G.F., S. Amillis, and G. Diallinas. (2017). Substrate Specificity of the FurE Transporter Is Determined by Cytoplasmic Terminal Domain Interactions. Genetics 207: 1387-1400. 28978674
Pinson, B., C. Napias, J. Chevallier, P.J.A. Van den Broek, and D. Brèthes. (1997). Characterization of the Saccharomyces cerevisiae cytosine transporter using energizable plasma membrane vesicles. J. Biol. Chem. 272: 28918-28924. 9360962
Pyrris, Y., G.F. Papadaki, E. Mikros, and G. Diallinas. (2024). The last two transmembrane helices in the APC-type FurE transporter act as an intramolecular chaperone essential for concentrative ER-exit. Microb Cell 11: 1-15. 38225947
Rapp, M., J. Schein, K.A. Hunt, V. Nalam, G.S. Mourad, and N.P. Schultes. (2016). The solute specificity profiles of nucleobase cation symporter 1 (NCS1) from Zea mays and Setaria viridis illustrate functional flexibility. Protoplasma 253: 611-623. 26022088
Rodionov, D.A., A.G. Vitreschak, A.A. Mironov, and M.S. Gelfand. (2002). Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J. Biol. Chem. 277: 48949-48959. 12376536
Rodionov, D.A., C. Yang, X. Li, I.A. Rodionova, Y. Wang, A.Y. Obraztsova, O.P. Zagnitko, R. Overbeek, M.F. Romine, S. Reed, J.K. Fredrickson, K.H. Nealson, and A.L. Osterman. (2010). Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. BMC Genomics 11: 494. 20836887
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. 18931129
Rodriguez, C., J.C. Bloch, and M.R. Chevallier. (1995). The immunodetected yeast purine-cytosine permease is not N-linked glycosylated, nor are glycosylation sequences required to have a functional permease. Yeast 11: 15-23. 7762297
Saier, M.H., Jr., B.H. Eng, S. Fard, J. Garg, D.A. Haggerty, W.J. Hutchinson, D.L. Jack, E.C. Lai, H.J. Liu, D.P. Nusinew, A.M. Omar, S.S. Pao, I.T. Paulsen, J.A. Quan, M. Sliwinski, T.-T. Tseng, S. Wachi, and G.B. Young. (1999). Phylogenetic characterization of novel transport protein families revealed by genome analyses. Biochim. Biophys. Acta 1422: 1-56. 10082980
Schein, J.R., K.A. Hunt, J.A. Minton, N.P. Schultes, and G.S. Mourad. (2013). The nucleobase cation symporter 1 of Chlamydomonas reinhardtii and that of the evolutionarily distant Arabidopsis thaliana display parallel function and establish a plant-specific solute transport profile. Plant Physiol. Biochem 70: 52-60. 23770594
Schultz, A.C., P. Nygaard, and H.H. Saxild. (2001). Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription activator. J. Bacteriol. 183: 3293-3302. 11344136
Smits, P.H.M., M. De Haan, C. Maat, and L.A. Grivell. (1994). The complete sequence of a 33 kb fragment on the right arm of chromosome II from Saccharomyces cerevisiae reveals 16 open reading frames, including ten new open reading frames, five previously identified genes and a homologue of the SCO1 gene. Yeast 10(Suppl A): S75-S80. 8091864
Stolz, J. and M. Vielreicher. (2003). Tpn1p, the plasma membrane vitamin B6 transporter of Saccharomyces cerevisiae. J. Biol. Chem. 278: 18990-18996. 12649274
Suzuki, S., and P.J. Henderson. (2006). The hydantoin transport protein from Microbacterium liquefaciens. J. Bacteriol. 188: 3329-3336. 16621827
Vlanti, A. and G. Diallinas. (2008). The Aspergillus nidulans FcyB cytosine-purine scavenger is highly expressed during germination and in reproductive compartments and is downregulated by endocytosis. Mol. Microbiol. 68: 959-977. 18384518
Wagner, R., J. de Montigny, P. de Wergifosse, J.L. Souciet, and S. Potier. (1998). The ORF YBL042 of Saccharomyces cerevisiae encodes a uridine permease. FEMS Microbiol. Lett. 159: 69-75. 9485596
Weyand, S., T. Shimamura, S. Yajima, S. Suzuki, O. Mirza, K. Krusong, E.P. Carpenter, N.G. Rutherford, J.M. Hadden, J. O'Reilly, P. Ma, M. Saidijam, S.G. Patching, R.J. Hope, H.T. Norbertczak, P.C. Roach, S. Iwata, P.J. Henderson, and A.D. Cameron. (2008). Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter. Science 322: 709-713. 18927357
Witz, S., B. Jung, S. Fürst, and T. Möhlmann. (2012). De novo pyrimidine nucleotide synthesis mainly occurs outside of plastids, but a previously undiscovered nucleobase importer provides substrates for the essential salvage pathway in Arabidopsis. Plant Cell 24: 1549-1559. 22474184
Witz, S., P. Panwar, M. Schober, J. Deppe, F.A. Pasha, M.J. Lemieux, and T. Möhlmann. (2014). Structure-function relationship of a plant NCS1 member--homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from Arabidopsis. PLoS One 9: e91343. 24621654
Yoo, H.S., T.S. Cunningham, and T.G. Cooper. (1992). The allantoin and uracil permease gene sequences of Saccharomyces cerevisiae are nearly identical. Yeast 8: 997-1006. 1293888
Zhang, J., K.M. Smith, T. Tackaberry, X. Sun, P. Carpenter, M.D. Slugoski, M.J. Robins, L.P. Nielsen, I. Nowak, S.A. Baldwin, J.D. Young, and C.E. Cass. (2006). Characterization of the transport mechanism and permeant binding profile of the uridine permease Fui1p of Saccharomyces cerevisiae. J. Biol. Chem. 281: 28210-28221. 16854981