Solute carrier family 46 member 3 (SLC46A3) is a protein that in humans is encoded by the SLC46A3 gene. Also referred to as FKSG16, the protein belongs to the major facilitator superfamily (MFS) and SLC46A family. Most commonly found in the plasma membrane and endoplasmic reticulum (ER), SLC46A3 is a multi-pass membrane protein with 11 α-helical transmembrane domains. It is mainly involved in the transport of small molecules across the membrane through the substrate translocation pores featured in the MFS domain. The protein is associated with breast and prostate cancer, hepatocellular carcinoma (HCC), papilloma, glioma, obesity, and SARS-CoV. Based on the differential expression of SLC46A3 in antibody-drug conjugate (ADC)-resistant cells and certain cancer cells, current research is focused on the potential of SLC46A3 as a prognostic biomarker and therapeutic target for cancer. While protein abundance is relatively low in humans, high expression has been detected particularly in the liver, small intestine, and kidney.
Gene The SLC46A3 gene, also known by its aliases solute carrier family 46 member 3 and FKSG16, is located at 13q12.3 on the reverse strand in humans. The gene spans 18,950 bases from 28,700,064 to 28,719,013 (GRCh38/hg38), flanked by POMP upstream and CYP51A1P2 downstream. SLC46A3 contains 6 exons and 5 introns. There are two paralogs for this gene, SLC46A1 and SLC46A2, and orthologs as distant as fungi. So far, more than 4580 single nucleotide polymorphisms (SNPs) for this gene have been identified. SLC46A3 is expressed at relatively low levels, about 0.5x the average gene. Gene expression is peculiarly high in the liver, small intestine, and kidney.
Variants SNPs are a very common type of genetic variation and are silent most of the time. However, certain SNPs in the conserved or functionally important regions of the gene may have adverse effects on gene expression and function. Some of the SNPs with potentially damaging effects identified in the coding sequence of SLC46A3 are shown in the table below. +SNPs of SLC46A3SNPmRNA positionAmino Acid PositionBase ChangeAmino Acid ChangeFunctionDescriptionrs14560674445541[T/G][M/R]missensestart codonrs74950187767946[A/G][N/S]missenseN-glycosylation siters776889950897119[T/G][C/G]missenseC-(X)2-C motifrs1403613207967142[G/A][G/D]missenseconserved substrate translocation porers7641984261322261[CT/-][C/F]frameshiftS-palmitoylation siters13737357931878446[T/C][Y/H]missenseYXXphi motif & STAP1 SH2 domain binding motifrs13423276151906455[G/A][S/N]missensephosphorylation & O-GlcNAc siters757225275 rs7519826481917459[T/G] [T/-][S/A] [S/Q]missense frameshiftphosphorylation & O-GlcNAc site f*The coordinates/positions are for GRCh38.p7.
SLC46A3 has multiple transcript variants produced by different promoter regions and alternative splicing. A total of 4 transcript variants are found in the RefSeq database. Variant 1 is most abundant. +Transcript Variants of SLC46A3Transcript VariantAccession numberLength (bp)Description1NM_181785.43302MANE select. Variant 1 encodes isoform a.2NM_001135919.22758Variant 2 encodes isoform b. It lacks a segment in the 3' coding region and the resulting frameshift causes isoform b to have a longer C-terminus than isoform a.3NM_001347960.13099Variant 3 also encodes isoform a. Variants 1 and 3 differ in their 5' untranslated regions (UTRs).X1XM_005266361.21845Variant X1 encodes isoform X1. *Lengths shown do not include introns.
Protein
Isoforms 3 isoforms have been reported for SLC46A3. Isoform a is MANE select and most abundant. All isoforms contain the MFS and MFS_1 domains as well as the 11 transmembrane regions. +Isoforms of the SLC46A3 ProteinIsoformAccession numberLength (aa)TranscriptaNP_861450.1 NP_001334889.14611,3bNP_001129391.14632X1XP_005266418.1463X1 *Lengths shown are for the precursor proteins.
Structure SLC46A3 is an integral membrane protein 461 amino acids (aa) of length with a molecular weight (MW) of 51.5 kDa. The basal isoelectric point (pI) for this protein is 5.56.
The protein contains 11 transmembrane domains in addition to domains MFS and MFS_1. MFS and MFS_1 domains largely overlap and contain 42 putative substrate translocation pores that are predicted to bind substrates for transmembrane transport. The substrate translocation pores have access to both sides of the membrane in an alternating fashion through a conformational change. SLC46A3 lacks charged and polar amino acids while containing an excess of nonpolar amino acids, particularly phenylalanine (Phe). The resulting hydrophobicity is mostly concentrated in the transmembrane regions for interactions with the fatty acid chains in the lipid bilayer. The transmembrane domains also have a shortage of proline (Pro), a helix breaker.
The protein sequence contains mixed, positive, and negative charge clusters, one of each, which are high in glutamine (Glu). The clusters are located outside the transmembrane regions, and thus are solvent-exposed. Two 0 runs that run through several transmembrane domains in addition to a +/* run in between two transmembrane domains are also present. The protein contains a C-(X)2-C motif (CLLC), which is mostly present in metal-binding proteins and oxidoreductases. A sorting-signal sequence motif, YXXphi, is also found at Tyr246 - Phe249 (YMLF) and Tyr446 - Leu449 (YELL). This Y-based sorting signal directs the trafficking within the endosomal and the secretory pathways of integral membrane proteins by interacting with the mu subunits of the adaptor protein (AP) complex. The signal-transducing adaptor protein 1 (STAP1) Src homology 2 (SH2) domain binding motif at Tyr446 - Ile450 (YELLI) is a phosphotyrosine (pTyr) pocket that serves as a docking site for the SH2 domain, which is central to tyrosine kinase signaling. Multiple periodicities typical of an α-helix (periods of 3.6 residues in the hydrophobicity) encompass transmembrane domains. 3 tandem repeats with core block lengths of 3 aa (GNYT, VSTF, STFI) are observed throughout the sequence.
Secondary
Based on results by Ali2D, the secondary structure of SLC46A3 is rich in α-helices with random coils in between. More precisely, the protein is predicted to be composed of 62.9% α-helix, 33.8% random coil, and 3.3% extended strand. The regions of α-helices span the majority of the transmembrane domains. The signal peptide is also predicted to form an α-helix, most likely in the h-region. The amphipathic α-helices possess a particular orientation with charged/polar and nonpolar residues on opposite sides of the helix mainly due to the hydrophobic effect.
Membrane topology of SLC46A3 shows the 11 α-helical transmembrane domains embedded in the membrane with the N-terminus oriented toward the extracellular region (or lumen of the ER) and the C-terminus extended to the cytoplasmic region.
The secondary structure of RNA holds both structural and functional significance. Among various secondary structure motifs, the stem-loop structure (hairpin loop) is often conserved across species due to its role in RNA folding, protecting structural stability, and providing recognition sites for RBPs. The 5' UTR region of SLC46A3 has 7 stem-loop structures identified and 3' UTR region a total of 10. The majority of the binding sites of RBPs and miRNAs given above are located at a stem-loop structure, which is also true for the poly(A) signal at the 3' end.
Tertiary
Model for the tertiary structure of SLC46A3 was constructed by I-TASSER based on a homologous crystal structure of the human organic anion transporter MFSD10 (Tetran) with a TM-score of 0.853. The structure contains a cluster of 17 α-helices that spans the membrane and random coils that connect those α-helices. Multiple ligand binding sites are also predicted to reside in the structure, including those for (2S)-2,3-dihydroxypropyl(7Z)-pentadec-7-enoate (78M), cholesterol hemisuccinate (Y01), and octyl glucose neopentyl glycol (37X). +Ligand Binding Sites of SLC46A3LigandC-scoreCluster SizeLigand Binding Site Residues78M0.053112, 116, 197, 198, 201, 204, 208Y010.05389, 241, 265, 269, 273, 391, 394, 39937X0.03286, 89, 90, 94, 109, 136
Regulation expression
Gene level
Promoter SLC46A3 carries 4 promoter regions that lead to different transcript variants as identified by ElDorado at Genomatix. Promoter A supports transcript variant 1 (GXT_2836199). +SLC46A3 PromotersPromoterNameStartEndLength (bp)TranscriptAGXP_19067828718802287200921291GXT_2775378, GXT_29165870, GXT_23385588, GXT_2836199, GXT_26222267, GXT_22739111, GXT_23500299BGXP_19067628714934287159731040GXT_2785139CGXP_19067928713272287143111040GXT_2781051DGXP_1967728704518287055571040GXT_2781071 *The coordinates are for GRCh38.
Transcription factors Transcription factors (TFs) bind to the promoter region of SLC46A3 and modulate the transcription of the gene. The table below shows a curated list of predicted TFs. MYC proto-oncogene (c-Myc), the strongest hit at Genomatix with a matrix similarity of 0.994, dimerizes with myc-associated factor X (MAX) to affect gene expression in a way that increases cell proliferation and cell metabolism. Its expression is highly amplified in the majority of human cancers, including Burkitt's lymphoma. The heterodimer can repress gene expression by binding to myc-interacting zinc finger protein 1 (MIZ1), which also binds to the promoter of SLC46A3. CCAAT-displacement protein (CDP) and nuclear transcription factor Y (NF-Y) have multiple binding sites within the promoter sequence (3 sites for CDP and 2 sites for NF-Y). CDP, also known as Cux1, is a transcriptional repressor. NF-Y is a heterotrimeric complex of three different subunits (NF-YA, NF-YB, NF-YC) that regulates gene expression, both positively and negatively, by binding to the CCAAT box. +SLC46A3 Transcription FactorsTranscription factorDescriptionMatrix similarityHIFhypoxia inducible factor0.989c-Mycmyelocytomatosis oncogene (c-Myc proto-oncogene)0.994GATA1GATA-binding factor 10.983PXR/RXRpregnane X receptor / retinoid X receptor heterodimer0.833RREB1Ras-responsive element binding protein 10.815TFCP2L1transcription factor CP2-like 1 (LBP-9)0.897ZNF34zinc finger protein 34 (KOX32)0.852MIZ1myc-interacting zinc finger protein 1 (ZBTB17)0.962RFX5regulatory factor X50.758CEBPBCCAAT/enhancer-binding protein beta0.959KLF2Kruppel-like factor 2 (LKLF)0.986CSRNP1cysteine/serine-rich nuclear protein 1 (AXUD1)1.000CDPCCAAT-displacement protein (CDP/Cux)0.983 0.949
0.955NF-Ynuclear transcription factor Y0.944 0.934ZNF692zinc finger protein 6920.855KAISOtranscription factor Kaiso (ZBTB33)0.991SP4transcription factor Sp40.908ZBTB24zinc finger and BTB domain containing 240.864E2F4E2F transcription factor 40.982
Tissue expression
RNAseq data show SLC46A3 most highly expressed in the liver, small intestine, and kidney and relatively low expression in the brain, skeletal muscle, salivary gland, placenta, and stomach. In fetuses of 10 – 20 weeks, the adrenal gland and intestine report high expression while the heart, kidney, lung, and stomach demonstrate the opposite. Microarray data from NCBI GEO present high expression in pancreatic islets, pituitary gland, lymph nodes, peripheral blood, and liver with percentile ranks of 75 or above. Conversely, tissues among the most lowly expressed levels of SLC46A3 include bronchial epithelial cells, caudate nucleus, superior cervical ganglion, smooth muscle, and colorectal adenocarcinoma, all with percentile ranks below 15. Immunohistochemistry supports expression of the gene in the liver and kidney, as well as in skin tissues, while immunoblotting (western blotting) provides evidence for protein abundance in the liver and tonsils, in addition to in papilloma and glioma cells.